To each their own, people can ship what they like! :) Haven't really tried it, but am not prone to ship mainstream ships much it seems (not by intent, it just happens that way).
I agree with you that it can be a way to be offensive about someone else's ship, which I don't ever think is okay. That's not a very nice thing to do.
I do think there are ships that aren't very good, that may be the only ship with exposure in a fandom and then, people ship what they're given. But, I don't think I would ever call it overrated, especially not to someone who likes the ship. That's just mean. Eg. I don't like Bughead or Olicity, but wouldn't talk about it with someone who likes those ships. What's the point?
I mean, Barry has great chemistry with a lot of the other characters in the Arrowverse, so yeah it's perfectly normal to be like 'hey, what about barry x that person'. This smol bean is a cutie pie so :)