For what it's worth, I do believe the intent behind Trek is secular-humanist and progressive at the very least; we're not exactly lacking when it comes to first-person sources on this subject. But in execution, the show speaks to universal values that fans across the political spectrum can appreciate -- and DS9 in particular often gives alternate points of view a voice because its writers were talented and just couldn't help but craft nuanced stories with multiple layers.
For more of my thoughts on the political orientation and appeal of Star Trek, check out the post here.
As you mentioned, the people behind the show certainly wanted to project that idea, but the needs of good story telling got in the way. We are constantly told such things as money don't exist, then shown that it does. Obviously resources are limited in the ST future, otherwise everyone would have a Galaxy class starship and a French vineyard. Money is just a way to allocate those resources.
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