I hated them with a passion all during the Young era when they always seemed to stand in the Cowboys way, but after he retired a lot of that hate dissipated. My hate flared up briefly during the TO era, but nothing like it was before. Now they suck so bad I don't really care anymore.
It's funny though, that even as I remember hating the 49ers so much back in the 90s, when I rewatched some of the classic Cowboys/49ers matchups recently, even the NFC championship loss in 94, I couldn't seem to revive that hate. I mostly look at that era with fondness now, and am even somewhat grateful that the 49ers were as good as they were because that quality of play, consistency, and rivalry back then dwarfs anything I see in the league today (eg I still say even the 49ers back then, whom I consider the 2nd best team of that era, would have still consistently beaten up the modern day weak dynasty that are the Pats).