I don't know but I suspect it is the following:
1 - Division rival. Prior to moving into the NFC West, I have pulled for the 9ers during their Superbowl runs.
2 - Sharpie incident
3 - Rams going from the hunted to also ran after the Greatest Show on Turf went away (see Mike Martz hatred to compare with current Harbaugh craze. And of course Mike Singletary craziness).
4 - Previous successes, though dated are constantly used as a way to trump any attempt to discuss teams current competitive advantages.
5 - Elitism due to past, though earned not taken well.
6 - Recent influx of 9ers fans over the past few years due to their recent success gives some an impression that many of their fans only want to talk now that things have picked up. (There are 9ers fans who have been here since mid-2000s when Nolan was coach but most have not showed up until Harbaugh took over). But we have folks that haven't shown up around here until after Mora left, so it cuts both ways, but that is just my thought.
Some have other reasons that go back decades of why they hate the 9ers. I cannot speak to those feelings. The list above is only my general thoughts on why there is so much pushback to any 9ers fans conversation. To me sometimes it seems to be a complex with some but maybe it is just good ole fan rivalry at its finest?
If you come with sword lowered, you are going to get skewered. If you come with shield raised, you are going to get called out as a troll. I would just assume that a hornet's nest will appear whenever posting as a rival fan. Too much in common as far as goals. If you were from another division or a non-threat to the fans here, maybe you get a majority of non-confrontational responses. Even the good guys (Ravens, Patriots, Saints and others) will not get 100% positive responses. Some folks just like being buttholes.