Admittedly, I haven't really looked to much into all the allegations against him, because I really don't care that much. But I'd have a hard time believing hearsay and gossip, especially when it comes out years after the fact. If he was arrested for sexual assault, that's one thing, but I don't think he should be vilified when no one knows the exact facts of the matter.
That said, he could be the worst man in the world and I'd still like Trek. I watch it for what's on screen, not because I have any interest in the lives of the producers/actors. Whether or not Gene Roddenberry is a nice human being doesn't change the inherent positive message that permeates through the series, and that's all that matters to me.