Yeah, that's what I was thinking too – there was lots of commentary about how people didn't like TNG when it premiered. I think it's just a given that people get attached to their vision of their favorite stories, and only want to see it continue as they knew it previously.
The thing that Discovery muddled a bit to me is that I got the sense in the DS9 era that Section 31 was actually operating "outside" of Starfleet and the Federation control? Like, maybe there was some kind of "top echelon" of Starfleet or the Federation that was still supplying it with resources but that it didn't actually have a mandate anywhere in normal structures and if Federation legislators knew about it they'd disavow or put a stop to it.