You do hear "it" more often, but I have a theory. If someone gives a compliment or does something nice for you, but it's a very ordinary thing, or a cliche, then you would say "I appreciate it". You say "it" because "it" (the compliment or gesture) is just "over there", away from both speaker and listener, in a pile with all the other cliches. It belongs to neither of you two people. If someone says or does something really nicely tailored to the situation, or wise, or well thought-out, then the remark belongs to the person who gave the compliment. So you say "I appreciate that", drawing attention to the fact that "that" is close to the person who gave the compliment.