The key word in your question is the word "defend." That suggests you have a position that puts you on the defensive. How about turning the tables? Ask questions that come from the perspective that you're from another planet and have observed this phenomenon of people getting flu shots and you're merely curious about the rationale behind it. Depending how patients respond, you could ask questions like:

Do you intend to get a flu shot this year?
Do you know anyone who has gotten one before (or yet)?
What's actually in a flu shot?
How do they know which flu bug to target?
How many vaccinated people end up getting the flu anyway?
What are some of the reactions people have to the shot?
What are other approaches to improving one's immune system?

Now, tell me again why you're getting a flu shot...

Obviously, it's difficult to script an interchange with a patient on a topic like this, but as you see, it's about asking questions. By the way, it's essential that you have answers to these questions, revealing your knowledge only when asked.

Many health behaviors are emotionally based. The Socratic approach above merely confronts a patient with the truth, which they may choose to reject. But the truth is the truth. Ultimately, it's the patient's decision. And if they opt to get a shot as a "rabbit's-foot-good-luck-charm-everybody's-doing-it-I-should-too," you probably won't be successful at preventing it. This year. However, you'll get them thinking in ways that could make a profound difference in the future.

Bill