Well, I kind of agree with you but then I don't. Every major U.S. sports has an all-star game of some sort. The biggest joke of an all-star game is the NBA. No way the fans should be allowed to vote the starters. Shaq as the starting center in the East and no Steve Nash starting for the West? Just absolutely stupid.
The majority of the selections in the NFL pro bowl are made by the players, which to me is the highest paid compliment to be voted in by your peers. Their has only been a few major injuries in the NFL pro bowl's history and sadly, Brees was probably the most significant to happen in quite some time. 
Personal opinions somewhat cloud judgement a lot of the times (even with the players). The pro bowl should be based on stats/performance alone, imo. Merrimen tests positive for riods and plays? Most players didn't agree with it. Some would call him a cheat. There are several cases of guys not going who clearly should have. Happens year after year, but who cares anyway.
Obviously I am a pats fan so I can give you the biggest screw job of them all. Not only did Asante lead the league in picks , he did it with every single one of the secondary starters out, for most the entire year. The patriots secondary allowed the fewest passing touchdown in the NFL in 2006 ( with half the starters out). Asante was the only starter out there, aside from Hobbs who played with broken wrist, and cast all year. Harrison and Wilson where out all year, so no help from them. Asante had several huge picks/plays in the post season. Injuries are a part of the game. But, if Asante performed that well with no starters around him, it is pretty clear the impact he has. A case can also be made for Ty Warren. Just an example of how people do get screwed. I know there are other players from other teams, but its pointless to research.
2006 stats
1 Asante Samuel NE 10 120 0 33 2 Champ Bailey DEN 10 162 1 70
3 Rashean Mathis JAC 8 146 0 55
4 Nnamdi Asomugha OAK 8 59 1 24
5 Charles Woodson GB 8 61 1 23
6 Walt Harris SF 8 84 1 42
7 Chris McAlister BAL 6 121 2 60
8 Kevin Kaesviharn CIN 6 24 0 22
9 Lito Sheppard PHI 6 157 1 102
10 Dawan Landry BAL 5 101 1 37
