A lot of it does have happy endings, or at least not overtly tragic ones. Spock do goes thru it, but ends up in a very good and important place, and is deeply at peace with himself for decades after all this stuff wraps. We don’t really see how Chapel wraps up, but she gets her MD and clearly stays in Starfleet, and so far as we can tell gets over Spock. And Pike gets “the illusion,” of course, which is about as happy as any person could be, given his circumstances.

Trek isn’t all happy events with clear closings; there were a lot of tragic endings in TOS, for example. Even TWOK is pretty much a tragedy, taken in isolation – Kirk’s hubris in deciding to exile Khan causes a lot of death and pain. Hell, even the resurrection of Spock comes at the loss of both the Enterprise and Kirk’s only son.

As long as the pain and tough times have narrative and character meaning, I’m more than OK with them happening because we know so much about how things do work out. Trek reminds, on the whole, a positive and uplifting look at how we can live.