I tend to agree, but there are two issues working agaonst Star Trek.

1. Successful media appeals to broad audiences by having something to appeal to every demographic. (E.g. Don’t like politics? Stay for the lasers.)
2. Good sci-fi (arguably stories in general) gives the best representation of both sides of a conflict, and lets them compete on their merits. So it’s possible to resonate with one side, then miss the critique (e.g. due to modest writing or selective hearing).

So while Star Trek tends to show progressive values winning in the end, many people can enjoy other aspects (e.g. military stories, relationships, and action) while ignoring the upshot.