Indeed, a more enlightened humanity, which strives to better itself, is not even remotely a bad idea.
The word "utopia" is a stumbling point, best moved past. But I will also throw into the mix that much research indicates that even today, money is not much of a motivator, once past the stage of providing basic needs.
If we have a future where the worst poverty is eliminated worldwide, freedom and enlightenment actually does increase, the birth rate begins to stabilize...umm yeah, these are good ideas.
Oh for sure, I don't think the part of Roddenberry's philosophy you mentioned is in question here, is it (it's a huge thread so maybe it is)?
I think it's the way it got handled in practice in TNG and later that's the problem. The semi-illogical extension that if the problems you mentioned are eliminated then suddenly everyone is okay with everything at all times and it gives them the right to preach about it is one of the biggest issues for me. People would still have interpersonal problems, personalities still may clash, etc. and Gene apparently had come to think that such issues would just simply not exist.