There is no drug interaction problem between the flu vaccine and Flagyl. But whether you get the vaccination while still taking the antibiotic may depend on why you are taking antibiotics. If you have a current infection, it is usually better to wait until that is cleared up before taking vaccines. But, each situation can be different, and this is a question that the doctor who prescribed the antibiotics should be asked to know what is right in your case.
Unless there is a specific reason your doctor wants you to wait, usually the only reason not to get a flu shot while taking antibiotics would be if you have an active infection with a high fever over 101 F. Get your flu shot unless you have a high fever, or the doctor recommends delaying the immunization due to your specific condition.