I just try to take it in stride - it is easier that way.
Unfortunately it is much easier to deal with the symptoms than the cause, particularly given that the cause is usually unknown, especially to the individual in question. For that reason, it is easier to attempt to correct them on small issues like this, rather than dealing with a larger issue like Islamophobia; sure there will be numerous issues like this, but after they see a trend in the type of responses they get across the subjects, those individuals usually at least subconsciously temper the outwards expression of such things (and hopefully, though doubtfully, even reconsider their position)... it is only when their baseless concerns are reinforced by positive responses or some real or imagined controversy that they kick up again.