Given the context, “cute story” is 100% patronizing / belittling. You need to employ some serious mental gymnastics to believe it’s being used in any other sense.
If you use it often AND you think OP used it sincerely, I think you may be unintentionally offending tons of people on HN without realizing.
If you want to express sincere compliment, there are many many words that are way better. "cute" is both literally and figuratively offensive. Which adult would like to be called "cute" (unless it's two sexually attracted people talking about each other) even if it was in a positive manner?
