Your surgeon is unfortunately spouting nonsense. This is like saying that it's not a good idea to have surgery (which I doubt your surgeon would say). It's certainly true that taking Flagyl for an extended period carries some risks, and you're better off if you don't need it. If it's what enables you to live a full, active life, though, then it's completely appropriate until/unless side effects make it a problem. 

This is one of the reasons most folks are (IMO) probably better off switching their care (after the post-op period) from their surgeon to to a *knowledgable* gastroenterologist.

Ideally, it is best not to take any antibiotic daily for a number of reasons. One reason is bacterial resistance from daily exposure. Another reason is the potential for side effects. Usually side effects go away if you stop the drug. Resistance is more difficult and you can wind up reducing your options in the long run. 

My GI does not want me to stay on any one antibiotic without a break, and I agree with him. His and my preference is to rotate antibiotics and stay off them whenever I can. This way I reduce both bacterial resistance and potential side effects.

Jan