I don't think it does. Most people evaluating these players for things like HOF, etc know what the pro bowl is. It's a frat in a way. Once you're in, you have to play your way out. When the votes were piling up for Favre, the Jets were looking pretty sharp and he was credited. It's no big deal. I think Romo had more of a probowl case this year than he did two years ago, but he's a the helm of a turbulent team and Eli Manning (who I actually think did deserve it to a degree) and kurt Warner were better stories (Brees was a no brainer).
there's no point in worrying about it...the wrong guy gets in a lot.