No. doctors are not always right, nor do they always have the tools needed. They may misdiagnose, they may not yet understand the disease correctly (plenty of those diseases), or there may just not be a good treatment (there are those diseases also). They are working from what they know and they may not know everything needed.
It's always worth giving the smarter doctors a shot at whatever you have, though. There is a lot of research being done. If they don't help, then move on if you wish.
I'd not discount them without trying, though. They are not all "pill doctors", and for many things, the right pills can help.
It's no more true that they don't know what they are doing, than it is that they know everything and should be trusted regardless.
In the case of the disease that started this thread, hasimoto's, that's pretty well understood. Trivial to suspect, trivial to diagnose and that's not one of the head-scratchers these days. TSH is up, free circulating thryoxin down. There's no need to resort to witch-doctoring with that one. Or, for that matter, with the other autoimmune disease, pernicious anemia. My main worry with doctors these days, is they're aging out of the activity. When they retire I've got to hunt down a new one!