I, too, agree with your pediatrician. 3 months is really early. Sometimes, for GI issues such as GERD (heart burn), they may recommend a small amount in a bottle, but generally speaking, he's right - they will eat when they are hungry.
Have you tried different bottles, different nipples? My kids had a few they refused. My niece would only take latex Platex nipples. My sister literally went through every other bottle on the market until finding it was the nipple, and she hated silicon.
Good luck! If it's any consolation, my son wouldn't take a bottle either until forced with me going back to work, and he did brilliantly.