Romo is arguably having the better season, but Favre is basically a living icon so it's clear why his vote total is through the roof.
I didn't even vote for Manning. :P Brady is a clear lock, but Manning has only been "pretty good" and certainly has competition from Anderson/Garrard/Roflsberger. Manning has done well enough that his name recognition will easily put him in anyway, but objectively speaking I'm not sure if he should be one of those four I mentioned. And no DM, Champ really hasn't been all that great this year. Or maybe he has, I don't follow the Broncos that much, but that Packers game sure sticks out like a sore thumb to me.
It's easy to vote for NBA all-stars because basketball is a far more individual game than football. That's not to say basketball isn't a team sport, but you can't tell me that Kobe Bryant or LeBron James don't single-handedly win games for their teams on occasion. It's especially hard for linemen and defensive players in football, where very few official stats are kept as compared to offensive skill positions. The only thing most people can base their opinion off, unless they've seen a majority of their games that year, is reputation.
I could see Donald Lee being the alternate, but him and Cooley are having a largely similar year so I wouldn't exactly say he was snubbed either. It's pretty much inarguable Witten is the clear #1.