I mean, look, I totally get their side--you are paying them for their knowledge which they accumulated from years of practicing and years of specialized training. You SHOULD largely trust them. But doctors are also often overworked, and may not always specialize in your particular area. You also obviously have a much more vested interest in the outcome as a patient, so there's a decent chance you'll spend much more time researching it than your doctor.
All of this to ask..."how can we strike a balance?" If one has doubts about what their doctor is telling them, they can always get another opinion. I just wish there was a better way to vet any research one might do on their own without the doctor getting upset that you continued to look into the matter instead of just taking their word on it when things don't improve.
Personally, I have an awesome doctor, but when I have these concerns I preface them by saying "I recognize this is internet research, and I trust your opinions on these things, but I had X, Y and Z questions." They have always been perfectly happy to answer my questions and address my concerns (as I would hope given what they bill my insurance for a 15 minute visit...)