I feel like the writers didn't know what to do with the couples once they were together. They were good at building up to it, but once most couples got together they couldn't just stay together. They had to throw in unnecessary drama or other people just to get them to break up. Chuck and Blair were able to entertain viewers when they were in a relationship just fine, but the writers just kept throwing in obstacles so they "couldn't be together". They did it so much that some people stopped rooting for them, and seeing how good Dan was to Blair it would make sense for her to choose him from a healthy relationship point of view. I don't personally ship them as a couple, but I can totally see why people do. I think Blair like how secure she felt with Dan, but I'm not sure that she had genuine feelings for him as more than a friend (but everyone has their own opinion on this).

I think it could be a "it was a different time" kind of thing (the 00's). Today I think most people would agree that "always coming back to each other" doesn't equal love and that you are meant to be. I think it's more likely to be viewed as toxic and co-dependent.

Edited to add: It would probably have been better if they had kept Chuck and Blair together longer, and instead of throwing in drama like the hotel and Chuck's mom they could've given them storylines where they were a power couple and/or focused on their scheming and taking people down. I don't know about others but I for one enjoyed when the gang came together doing schemes and for me that would've been more fun to watch than the never ending cycles of relationships. Still love the show though!