I think you're reading too much into it.
It's very easy to find PC messages and left-wing slants in any form of entertainment; movies, TV, music, books, without expressly looking to see if you can find it.
Along with Enterprise, some of my favorite shows are -
Buffy the Vampire Slayer - demons, monsters, witches, a major character is a lesbian, uncomplimentary religious references
Angel - same as Buffy
NYPD Blue - nudity, language, PC storylines
Friends - co-habitation, gay references, sex references, sleeping around
I could keep going. Now, could I stop watching these shows because there are things I don't agree with, sure. But I enjoy a well-written show with a good storyline, which the first 3 are, and Friends is funny as hell. The point is, if we tune out and turn off every single reference we find semi-objectionable, we'd never find any time to wind down and relax.
My advice, if you like Enterprise, watch it, enjoy it, and stop worrying about this reference or that reference. We all have to take a break from the fight sometime.
I think that some of the best plots in Star Trek, as well as Science fiction in general, have been those that actually did deal, in some metaphorical way, with actual political and social issues that we face. Those that make some kind of statement or ask us to question the way we view things are those that will endure. A very classic episode from TOS was titled something like 'Let this be your Last Graveyard'. Briefly, this episode dealt quite bluntly with issues of racism and hate and stated that racial violence could spell the end of our civilization. This was back in the 70's I think when racial tensions were really becoming a problem.
Now, there was a Star Trek Enterprise episode recently that featured a set of vulcans who were practicing mind-melds with eachother, a practice found disgusting by vulcan society at large. This practice also exposed some of them to a particular mental disease. Captain Archer criticized the Vulcan leaders for not doing more to find a cure for this disease, accusing them of a sort of bigotry. This was a metaphor for the issue of AIDS and homosexuality today. The point was that those who oppose increased funding for AIDS research do so on the basis of bigoted intolerance for homosexuals. Now, let me emphasize that I don't agree with the political point that was being made. However, I think this was a good episode because of the artistry with which the point is made.
so, to sum up, you don't have to agree with the liberal-atheist politics of Star Trek to enjoy it.