I think it had more to do with the shows becoming more conservative and living on TOS' reputation of being progressive. I think the people who ran the shows were more conservative than their 1960's counterparts.
I don't dispute that one bit. It was actually a combination. TOS was made at a very progressive time in the US, and pushed the envelope with some thinly veiled social commentary in several episodes. But what most people don't realize/remember, is by the time TNG hit the scene the US had swung to a far more conservative/constrictive place, and stayed there for a long time. Enterprise was the only series that was being produced at a time where they might have been able to pull it off, but the court of public opinion still had not completely come full circle on the LGBT community. Add to the the fact that Enterprise's ratings where in the tank most weeks and it just didn't make for an environment for risk taking.