"Used to" is normally referring to something that was done in the past, but is no longer done. "I used to think John was a pretty smart guy." This implies that I no longer think John is smart. "Used to" can also mean, "accustomed to" or "familiar with" "After people have known me for a while they get used to my corny sense of humor." "Usually" means most of the time. "I usually don't listen to negative people" A habit is something you do without thinking about it. "After you have been driving for years, your driving becomes a habit more than a decision." A habit can also be something you feel compelled to do because you have done it for such a long time. "I have a bad habit of eating too late at night."

"Used to" indicates a past habit which you don't do anymore. "Usually" indicates a present habit. "Usually" is also an adverb - it describes how often you do an action. "Habit" is a noun.