This feels like a generational thing as much as anything else at this point.
The context in which Section 31 was invented was still only a few years after Oliver North and his people pulled off Iran-contra, and not so much farther from when G. Gordon Liddy and his White House Plumbers pulled off Watergate, and that sort of thing is what Section 31 was referencing. Groups that aren't just secretive in the sense that some agencies do a lot of classified stuff, but are 100% illegal and are literally just groups of public servants running crime syndicates out of government offices.
The problem is that in the post-9/11 era, any kind of distinction like that is just gone, and people (pop culture especially) have completely absorbed the mindset that lawless and unaccountable is just how the entire intelligence/security community is supposed to be. You wouldn't want Jack Bauer to not be able to torture people, would you? That's how he saves the day! You wouldn't want Jack Bauer to have to answer to elected officials, would you? All politicians are corrupt and then he'd be working for Charles Logan!
So we've ended up in this world where the security state, from the lowest sheriff's department all the way up to the CIA, is effectively a law unto itself and most people have given up even pretending that it can be or should be otherwise. And in Star Trek, this is reflected as "oh yeah, Section 31 is just the Federation's intelligence agency. How else would an intelligence agency be?"