If your aren't feeling good about what a doctor is telling you, ask questions - challenge them even. Doctors make a decent living - they should be able to explain and defend their recommendations to a parent in a way that makes sense. If you are not satisfied with the information you are receiving, get a second opinion and don't apologize for it.
No one is going to ultimately look out for the best interests of your child better than you. Don't be afraid to get second opinions.
Here are some examples of when we have sought out second opinions:
Perinatologist: The perinatologist we were initially referred to creeped us out. We did not like the way she approached us and got the clear sense that she was actually pushing her values on us - values that we did not share. We asked everyone we knew for recommendations and found a WONDERFUL medical group that ultimately delivered our daughter.
Urologist: The urologist we were initially sent to rubbed me the wrong way. She seemed "put out" by my gentle (really) questions and at one point snapped at me during an exam. We asked our pediatrician for a new referral and ended up with a Urologist whom we greatly admired.
Orthopedics: We really like our orthopedic team however we want to explore all options when it comes to treating Annie's spine. Our orthos seem to have "their way" of doing things so we have made an appointment to take Annie to Shriners in LA for a second opinion. Again, we have no problem with our ortho team but for the sake of our own consciences we feel we need to get a friendly second opinion.