I think there was a tremendous cynicism about McGwire before he retired -- at least in terms of his qualifications to be a first ballot Hall of Famer. I think I've laid out that argument and stand by my belief that even without a steroids controversy, McGwire is, historically, not a first ballot sort of player.
But it also seems clear to me that as the steriods scandal has unwound itself, long after the summer of 98, McGwire has been an understandable suspect to most people with regard to that issue.
I don't think it matters to most people that he's never admitted to anything (Bonds and Clemens haven't admitted to anything, and there's obviously a wide-spread belief about their cheating) or that nobody's ever directly implicated him in anything (other than Canseco, of course; nobody had implicated Palmeiro other than Canseco, IIRC). I think the issue is that McGwire sure appears to be a model suspect for someone using steroids or HGH (along with Andro). When McGwire gave his wishy-washy, Fifth Amendment-clouded "testimony" before Congress, I think those who wondered about his use of steroids or HGH became convinced of Canseco's allegation.
This isn't a court of law; such inferences from vague testimony and Fifth Amendment assertions is perfectly understandable in the court of public opinion. Hall of Fame voting, when you get right down to it, is largely a matter of opinion (at least the opinions of baseball writers) and those are the very people who may have been most offended by McGwire's evasiveness in Washington.
Personally, I don't see McGwire's non-election in 2007 as some sort of unprecedented omission or a hideous injustice. I would see it that way if the Congressional hearing had never happened, but I'm particularly inclined to see it that way after that hearing. Whether it was permissible or not at the time, it seems clear to me that using steroids or HGH (at any time) is cheating. I believe that Mark McGwire cheated and I don't think a cheater should be rewarded with the very highest honor in the game.