Is it still uncool to like both? The Atari ST had objectively worse game graphics and sound, but it was better than the Amiga for things like MIDI and DTP.
My 30 year old grudge has more to with the one rich kid in my school who actually owned an Atari ST. It was slightly more expensive than the Amiga, which he loved to point out.
The reason so many people who had an Amiga are (still) salty over the ST is that lots of games were ported straight from the ST without taking any advantage of the extra power of the Amiga besides audio. While the publishers are to blame here, the ST is the easy target.
Had the ST not existed, those games would have likely targeted the Amiga hardware first and foremost, and been far better as a result (proper scrolling, higher framerates, more and better colors, etc.). But again, the ST is not to blame for that.
Similar thing happened to MSX and Amstrad CPC owners with ZX Spectrum ports. These days all these machines have healthy homebrew scenes that show how nice the hardware really is. I still can't believe Dread and Metro Siege are real Amiga games. And Dread has an ST port, and that's a good thing.
A large portion of the games were developed for both systems simultaneously, often without the Amiga version taking advantage of the machine's better capabilities. Some games had better music on the Atari ST, but largely because of the abilities of the composers.