I never know what to make of this one. On the one hand, it's a reasonably diverting piece of entertainment (especially if you like the doctor) and plays with the matrix style notion of reality in a fun way (though not remotely original) but on the other, it doesn't really make much sense.
Firstly, I think it's far too early in the series to start having the doctor question the nature of his reality and secondly, the whole thing just feels like a throw-away episode that embodies the reset mentality of Voyager. So much so that when the doctor meets Barclay again later in the series, he behaves as though he has no idea who this Barclay chap is (um, he's the dude you spent all that time with in Projections, mate).
A fun romp but essentially worthless in the grand scheme of things. If you never saw this episode, it would make little difference to your Voyager experience (though you could say that about a few episodes). The doctor's journey to self-aware sapience is better explored in other episodes.