Diflucan is pregnancy category "C", which means it *may* have side-effects on the fetus, but may be prescribed when the benefits to the mother outweigh the risks.
According to the FDA pregnancy category "C" means: Animal reproduction studies have shown an adverse effect on the fetus and there are no adequate and well-controlled studies in humans, but potential benefits may warrant use of the drug in pregnant women despite potential risks.
It *may* be harmful, but so would being hit by a bus. The risks of a long term infection of harming the fetus are far more well established, which is likely why the doctor chose to prescribe meds to clear up the infection now. Vaginal infections are known to lead to problems in pregnancy, while Diflucan *may* cause problems. It's a risk management issue.
Only you can decide whether the risk of an ongoing infection or alternative treatments is worth it to YOU and YOUR baby, or whether you will keep taking the Diflucan - or any other meds your doc prescribes.
If you don't trust your doc to do what's best for you and the baby, however, then you probably need a new doc. Trusting Dr. Google/Dr. Internet is generally a bad idea, though it can at least arm you with information you need to discuss with your doc.
Good luck.