In the eight years it took me to section-hike all the AT, I only stayed in six shelters. I just can't sleep well in them. Reasons include: The slightest noise or movement wakes me up, I toss/turn a lot myself so I'm always concerned about waking other hikers, I need to use the woods a couple times a night and I worry about waking others, and when I hike with my dawg I'm aware many shelter dwellers don't want to share space with her.
The shelters provide something of value to many and I'm not against them (actually, I help maintain one as a volunteer), just choose not to sleep in them.
Typically, I'll camp near a shelter (but not right next to one) to take advantage of the water source, privy if there is one, a place to cook/eat, and the comaraderie. But come bedtime I'm outta there.
P.S.: I have the same view for similar reasons toward dormitory-like situations in hostels and in the White Mt. huts, tho due to weather concerns I've used the latter (didn't get much sleep).