Well, these are usually harem protagonists, and Kyousuke hardly looked like one when introduced. Besides, playing the violin does require some brains, I'd say. A person trained in elaborate techniques of an art that supposes emotional input ought to be more perceptive to emotions.
And the "see them as males" part was a pure figure of speech on my part. Of course, Kyousuke would never see Sayaka as boy (though if he did, your notion concerning anime teenage males would fit him 200%
).