I think some people have more of a problem with this because it isn't allegorical at all - it's set in our world, with our political and governmental institutions, so it comes across as a polemic. That's always going to turn some people off because they feel they're being lectured at, not entertained.
If it was set on planet Sigma Alpha IX and the Prebulicans were brutally arresting and deporting immigrants to Xecomi you probably wouldn't bat an eyelid.
But Star Trek has always had room for allegory and polemic, particularly DS9. I'm perfectly comfortable with this.
Our world is pretty shit for a lot of people and showing characters fight for a better one that they know can exist is pretty much Star Trek's mission statement.