Check out the links provided, for sure; and follow your instincts.
If you HAVE to stay with this doctor, and suspect that the reflux might be related to dairy and/or soy allergies via your diet, you may be able to address the reflux without meds. But, if you need meds, you will need to get your doctor to make a referral for you, or at least prescribe some meds (you'll need to be vigilant that he's not giving them at placebo levels).
Personally, having had a baby with severe reflux-- and multiple food allergies -- and a very educated and supportive Pediatrician who knows her stuff on both issues ---- if I were you, I'd start calling around to other Peds and see if you can find a more knowledgeable one.
Questions to ask:
1. Do you have a lactation consultant on staff? (What do you do if a mother is having breastfeeding difficulties? Did you/your wife breastfeed?)
2. What is your experience with reflux, infant food allergies, and MSPI (Milk Soy Protein Intolerance)?
If the doctor doesn't seem to be "up" on breastfeeding, s/he may not be supportive of that while trying to resolve the reflux (i.e. may try to treat it with formula, or thickened feeds etc.).
If the doctor doesn't seem to be "up" on reflux, and/or food allergies, then they may give you suspect advice on that front (i.e., suggest a lactose free formula while EPing to check for a cow's milk allergy - when really the solution is for mother to remove dairy entirely from HER diet and no need to EP and lactose free formula doesn't do anything for food allergic infants).