Generally speaking, getting a flu may not cause the feeling of hurt in the eyes. If you really feel hurt in the eyes, it may be that the viruses of the flu have infected the eyes, which is a very rare case. Feeling eyes hurt can be caused by some other reasons. For example, you may get conjunctivitis, keratitis, or some other eye problems. Or it is possibly that you have used your eyes for too long a time without any rest, thus the optical nerves and muscles get tired and feel hurt. You should have adequate rest and sleep, and do some eye exercises to reduce the pain the your eyes. You can also use some anti-fatigue eye drops.