Tyler Kepner's NY Times article is well-worth a read. Your money quote:
Maybe Jeff Bagwell took steroids, maybe not. Bagwell played most of his career before testing, but so did everybody else who has ever appeared on a Hall of Fame ballot.
As far as I can tell, the only thing Bagwell is guilty of is playing in an era when his union fought against cleaning up the game. The legacy of that shameful stance is that baseless suspicion may now keep some deserving players, like Bagwell, out of the Hall of Fame.