I did a drug interaction checker on these meds. What it said is that H2 blockers such as Zantac can cause the Naproxen to dissolve early (in the stomach instead of the small intestines). It states they shouldn't be taken at the same time. I also decided to check how Naproxen interacts with Proton Pump Inhibitors (such as Prevacid) and anti-acids (such as Tums). It was also recommended not to take Naproxen with these as well due to concerns about absorption of the Naproxen.
The problem is - Naproxen can cause reflux symptoms or worsen them. It is fairly standard practice to prescribe both in order to try to keep the pain in check but not wind up with worsening reflux.
The big concern with these meds interacting though is a lessening of effectiveness for the pain killer. It isn't necessarily a dangerous interaction but one where you may not get the pain control you need.
You have valid concerns though that you should address with both your doctor and your pharmacist. Either or both might have suggestions as to when it would be best to take each one. Or may be able to give you information about how it's been used in practice.