Well yeah, Roddenberry had his weaknesses was far from perfect, and the writing on TOS and TNG didn't always reflect his noble intentions. But I don't see how that invalidates the message of the show or anything.
I'm not saying it invalidates it, I'm just saying that even though he created Star trek, he wasn't good for it. Imagine if DC Fontana and David Gerrold were able to work on the show without Gene and his lawyer always butting in and telling them what to do and what not to do. Michael Piller always described this situation as "Gene's Box", where as long as you work under Gene, you have to abide by his rules of Star Trek. They basically amounted to "Humanity is perfect and there is no conflict. Now go create drama."
If Gene himself didn't care that much for Star Trek's message, why was he so darn insistent that this message be taken to the most serious degree with the other writers?