I've never been sure what to think of Gene, largely because a lot of what's said about him is opinion, and subjective, and few sources are ever quoted. For example, many people in this thread have alluded to his ill-judged ideas of utopia and human perfection - people no longer mourn loss, for example - but what are the sources?
All that said, having just read the season one TNG Writer's and Director's Guide (while there are references to improved humans, they're certainly not to the extreme extent mentioned upthread) it's pretty clear his attitudes toward women were...poor, to say the least. Not Ian Fleming bad, but certainly enough to instill a queasy feeling.
Consciously, subconsciously, or degrees of both, he was a hypocrite, but does that detract from Trek for me? No, because he was never a prominent figure for me; the idea itself mattered far more than who first germinated it. if it were proven he was a sexual predator, however, that would be a little more difficult.
Oh, and every writer puts something of themselves, and those around them, into their characters, and any saying otherwise are lying. The trick is not to make it obvious.
