I didn't see anyone saying they say "I enjoyed your Bob/Ted story even though I think Bob/Ted shippers are dumb and Bob/Ted is inherently inclined to be sucky" and view it as a compliment.

But some people were saying that "I liked this story even though I don't usually read [pairing/trope/whatever]" was the equivalent of the above, and lots of people saying that to them it's a huge compliment. I'm one of them. If someone liked my story despite not shipping the pairing or whatever, that says a lot more to me than someone who's already primed to love every story with that pairing that crosses their path just because they can't get enough of their OTP.