Well let's see, you can say it's self-deprecating... and it's been a while since I've seen any Charlie Brown, but the lasting impression I had was that poor Charlie was too trusting, and he got screwed over, he was the victim, and Lucy was the villain. So there's one thing I don't like about JMS. He's always the victim. Besides, if you thought JMS was a 'dupe' why would you be volunteering your effort on his behalf. Seems like you would subscribe to a sympathetic take on Charlie Brown's field goals as well.
As for the Breaking Bad reference... why are you having troubles understanding my issue? He comes off to me like he took that as a slight. Maybe he's mad that Star Trek got a whole spec script discussion scene? I don't know. But instead of "Hey a great show referenced my show and it made me smile" we get complaining about how obscure B5 has become.
Also glancing at the guy's twitter he's arguing with anyone who is saying Netflix is more important than cable, "As a rerun, B5 would be shoved to the back on Netfilx; on cable folks who don't know it can bump into it". For someone who was in on pretty much the ground floor of the Internet, he's coming off as pretty out of touch.