It's a really good question and it's sad you're only getting defensive, dismissive answers. Sometimes a fandom becomes a vanguard against anything that even sounds critical.

I think it's easy to see why the lesser of the kingdom's would've stayed loyal to the Targaryens--either they were benefiting greatly from the continent-wide economic system, or they were too militarily weak to assert their own independence. But what about a place like The Reach, which could cut its food supply to King's Landing and threaten the crown with a powerful military?

Well, there'd have to be some sort of alliance between them and other loyalist kingdoms that was too valuable to break. Maybe Dorne and The Reach had an alliance (just making this up), and The Reach didn't want to lose out on a lucrative trade relationship by attempting to usurp the crown. They think, "If I go after the throne the Dornish will be our enemies, and we need them." So they don't do it. Now say the North wanted to rebel; they'd have to calculate that The Reach and Dorne were inseparable and Dorne would be with the crown from the start, with no chance of changing their minds. This would quell the North.

Then maybe the Iron islands wants to rebel, but the North says "No, Dorne and the Reach will never budge. Count us out." So the Iron Islands knows if they rebel, they have to at least fight those three kingdoms.

I'm making this up, but you see my point. It's perfectly reasonable to hold out hope GRRM might explain something along these lines in Fire & Blood, which would make it all make sense. What he probably won't explain: Why the Targaryens didn't install direct family relations at the head of all Seven Kingdoms, which would nullify this whole question (as England did with its Dukes and duchies); why the citizenry just said "Duh, okay den" when the ROYAL FAMILY was wiped out (as if the kingship was not inherently a religious title bestowed by god).

None of these questions are plotholes, by the way. World-holes I guess you could call them. Nothing too catastrophic anyway--always remember that no matter how absurd a fictional situation sounds, as long as it's not magical it's probably happened at least twice in real life.