Because Starfleet is supposed to be a multi-species organization, not a human-led empire. That we're told that Starfleet is an equal-opportunity service but shown only humans could be seen as analogous to being told that any person could go to a given college (or serve in a military rank, be doctors, ect.) and then just see a bunch of white dudes.
The fact of the matter is, within the Trekverse aliens are the allegorical reference to non-whites and/or people from non-western cultures. That's what they're there for. It might matter a lot that Michael Burnham is a black captain to viewers, but it doesn't matter one whit to those within the show's universe, because it's an explicitly race blind setting. If you want to actually have stories about tolerance and inclusion, you have to show characters bridging gaps that are hard for them, not doing what comes as second nature.
Edit: I should say that I think there are plenty of settings where having all/almost all humans is completely forgivable. But Star Trek is not one of them. It's been built into the DNA of the show by this point that we'll all join hands into one big mélange of culture which spreads across the galaxy. Not actually showing this in practice betrays this ideal.
I think that's fair. If you are going to tell a story about a organization with 150 member worlds (or in S3's case, an organization with 30 member worlds that Earth is no longer a part of), you should try to make the populations consistent with that backdrop, though it will always be a bit human centric because it's a TV show for a human audience.
Also totally agree with using non-humans as a way to tell stories about discrimination, DS9 did a great job on this with Odo and Voyager did an OK job with the Doctor. Though I will say my favorite was a more direct story about racism, it was a DS9 episode where Sisko has a vision about being a magazine writer in the 50s. Really powerful stuff.