Two reasons, in my opinion:
1. For a Cowboys player to get in, he has to be more than just great. I mean, look at Cowboys in the HOF, like Lilly, Allen, Roger, Troy, Emmitt, etc.
All like 10-time Pro Bowlers, or league's leading rusher, or be the winning qb on 3 SBs, or absolutely dominate their position. Meanwhile players like Lynn Swann get in because they just happened to be on a team that won 4 SBs, despite not having stats nearly as good as snubbed players like Tony Hill.
Woodson has 5 Pro Bowls, if he had 8 or so he'd be in probably.
2. Woodson was very good at everything related to his position - tackles, interceptions, games played, Pro Bowls, etc. But not a standout in any one area, if he'd had 50 ints, for example. Or if he'd had a signature play, like 1 90-yard pick-6 in a SB. Even though being very good in multiple areas is probably more valuable than just being a sack master or such.
Not saying there may not be an anti-Cowboys bias, I don't know if there is or there is not. Could be a third reason, who knows?