They are quite similar, but the etymology is different.
A "Kathedrale" is a church of a bishop's see. "Münster" and "Dom" not necessarily, like the Ulmer Münster and the Petersdom (St. Peter's basilica).
"Dom" comes from Latin "domus dei" - "house of God". "Münster" was derived from Latin "monasterium" - monastery. In English, it formed the word "minster" (at least in British English).
Basically, most churches simply have their names and there just happen to be 3 names for bigger churches. When you talk about churches in general, you still call them "Kirche", sometimes "Kathedrale" if you want to stress that it's a monumental building. So this should answer the habit part of your question. In everyday talking, people might even call a "Dom" or a "Münster" a "Kathedrale" - just because this is the most common word.