My problem isn't so much with PEDs users or what they did per se. The guys who we know of are the ones who got caught, but realistically, far, far more were using them (and likely still are). The culture of the sport simply made that acceptable to them. I'm not happy that the steroid era happened, but it happened, and it is what it is.
What bugs me is the deny-and-blame attitude that several of the roid-era players take. Clemens is probably the best example. It seems very obvious that he juiced, but he gets up and raises a huge stink and say s everyone is just out to get him. Look douchenozzle, nobody would be "out to get you" if they didn't have a damn good reason to. Nobody is witch hunting your contemporaries who put up similar numbers, with no apparent cheating -- Maddux, Pedro, etc. People are out to get you because they damn well know you did it. If he would just say "yup, I did it, lots of us did, and it wasn't against the rules at the time" then fine, you're in the HoF. But the whiny, child-like display is what makes me not want him in the Hall.
Absolutely everything I just said applies doubly to Lance Armstrong, perhaps my least favorite athlete ever (there are other reasons besides the juicing, but his reaction to the investigations made it much, much worse).