They're permanently locked away, so he really is alone. And he did mumble some explanation to Amy. By the way, Matt Smith's delivery here didn't appeal to me. After what we've seen in The End of Time, which from the Doctor's point of view was only a few days ago, the line came off as oddly detached and sort of goofy.
I think Eccleston and Tennant conveyed the Doctor's tragic background much better when they told their companions about the Time War.
Well, yeah, because Eleven wasn't trying to convey his tragic background. He was trying to gloss over it because he doesn't want to talk about it. You're holding it against Smith for not delivering a moving performance where he once again mourns the Time Lords when the entire point of his character's agenda was to avoid doing just that.
"Have you ever run away from something, just because you could?" "Yes. Once." What's he referring to?
Presumably, he's referring to that time he stole an obsolete Type-40 TARDIS from Gallifrey and started wandering time and space for a while. He only did it once -- and he's still going at it.

Excellent episode, but a lot of unanswered questions (and not in a good way):
1. How was every other single nation on the entire world, from Nigeria to Scotland, able to abandon the Earth in working spaceships but not Great Britain?
Why does that matter to the story? I mean, I'm sure there's an interesting story there, too, but it's really not important to this story, now is it? All you need to know for this story is, Starship U.K. is the United Kingdom's future incarnation, created out of desperation when the other nations had fled the Earth.
2. Isn't Scotland part of the United Kingdom? Did the blacks in the United States go off on a separate spaceship than the whites? Seemed like a rather nasty sentiment disguised as a joke.
Well, first off, African-Americans don't have their own separate country within the United States the way the Scots have Scotland within the United Kingdom.
Secondly, in what sense is it a "nasty" sentiment, especially since it's quite plausible that at some point in real life, Scotland could become an independent state? Is it nasty against the Scots, or nasty against the United Kingdom?
Thirdly: Sheesh, lighten up. The point of the joke wasn't to say that Scotland was right or wrong for going off on their own, just to say that the Scots and the English will probably always have a bit of a standoffish relationship and to have a laugh at that fact.
3. What the bloody hell were the Smilers? Where did they come from and what was their function? Why were the hooded people able to turn their heads around? This all made no sense.What was the point?
We saw their function. They're the secret police, the enforcers. Created by the government. Some were fully robotic, and some were cybernetic. Do you really need this spelled out for you when you saw it?
There's an old saying in storytelling: Show, don't tell.
5. How does Winston Churchill have a direct line to the Doctor?
Presumably the same way Martha Jones does -- the Doctor worked his magic on a period phone and installed a device on it that would let it contact the TARDIS through time. Again, do you really need everything spelled out for you when you've already seen something similar explained in previous episodes?
7. Why do we need to see such a nasty, petty, unforgiving side of the Doctor?
Because the Doctor isn't perfect and to portray him as such would be a disservice to the character and to the audience.
Although I mostly enjoyed the episode, I agree that the "hug" scene was a bit out of place and premature. In the previous episode, we see how Amelia, a 7-year-old orphan girl with a neglectful aunt in an unfamiliar place (England), puts her trust in a man who promises he will return shortly, then abandons her for 12 years (through no fault of his own, but still). Then he shows up, and proceeds to abandon her again for 2 more years (less excusable, since his TARDIS is in full working order) and when he returns, he dismisses his mistake with an "oops". I found Amy's suspicious demeanour at the end of 5x01 appropriate, i.e. she might be thinking "the Doctor has hurt me once before, despite promising not to, so who knows what he is up to this time?"
Fast-forward only one episode, and it seems Amy has warmed to the Doctor far too fast. I was hoping to see some more exploration of the unresolved issues between Amy and the Doctor. Maybe we'll see it in later episodes.
I think the key here is Amy realizing that the Doctor is the last of his kind. I think her understanding of just who and what he is shifted at that point, and prompted her to realize just how lonely he must truly be, and how painful the situation with the space whale must have been for him.
But I also don't think that the fact that she chose to express her affection for him at a time when she sensed he needed some emotional reassurance means that the tension and secrets and suspicion is gone, either. In real life, people often have unresolved conflicts that can be put on the back-burner when other issues come to the forefront; that doesn't mean that they're gone or it's a discontinuity, it just means that people are multi-dimensional.
Amy adjusted quite well to being in the future, I'm not sure if i like or dislike this. On one hand, it is nice to see a competent companion who doesn't freak out at future stuff and can adjust well. On the other hand, a 21st century human would pretty much freak out at the future stuff and get into a lot of trouble and may have trouble adjusting.
Wouldn't that really just depend on the individual? I feel like you're trying to make a big, sweeping statement about how all people from today would react to something, and it just seems kind of silly to me to claim that. Some 21st Century Humans would certainly freak out; others wouldn't.
I seriously think the Doctor overreacted with her though, he was really harsh on her, too harsh. Kinda mean honestly.
Yeah. But I also think the thing to remember about the Doctor is that, 1. he has a that harsh streak to him -- that's always been a part of who he is, and 2. he's adjusting to having a companion again after traveling what, for all we know, could have been decades for him between "Journey's End" and "The Eleventh Hour."
Average.
Why did the doctor send Amy to wonder off five minutes into her first TARDIS ride?
Exactly, making on my point above, this seemed odd to me, a brand new companion, never been to the future, has no idea what is going on, and the Doctor sends her on her merry way like she is a seasoned pro. Very irresponsible of the Doctor.
And how is this any different from just bringing Rose to the year 5 Billion and letting her wander about Platform One? The Doctor always thrusts his companions into situations.
And people who still think Amy is romantically ga-ga over the Doctor at this point are totally barmy.
And what makes you think she lacks romantic feelings for him from this episode? (I find that claim especially amusing, considering that others are claiming that Amy is warming up to the Doctor too fast -- wouldn't someone harboring romantic feelings for somebody warm up to him/her faster than if they didn't?)
And what, exactly, does "romantically ga-ga" mean? Why do you frame the experience of having romantic feelings for someone in disempowering terms? Having feelings for someone doesn't mean you're blind to their nature or choices or faults, nor does it mean you lose self-initiative.
* * *
As for me:
Loved it. It's not "Human Nature" or "The Girl in the Fireplace," but few things are. It's definitely right up there with the best of nuWho.
Also, Amy is really, really growing on me. She's officially displaced Martha as my second favorite companion, and if she keeps showing the kind of quick insight, assertiveness, and compassion and affection she showed in this episode, I suspect she may even displace Rose as my favorite companion.
And I am a diehard Rose/Doctor shipper, do recall.