Despite both have the same meaning, in my opinion Entender is a more usual verb than comprender, a little bit. And there is one different meaning that I don't know if the dictionary has.
We can say that one person "entiende", when this person likes people of his of her same sex. But not in a rude way, if someone doesn't want to ask directly the tastes of other person, he or she can say, "tú entiendes?"