I think its the dichotomy of his personality. He is completely insane, a total psychopath and a very evil guy, but he likes good classical music, gourmet cooking, classical Italian architecture. He is a serial killer and a cannibal, but yet well educated and well mannered. He apparently is capable of killing or maiming anybody at the drop of a hat yet he treats Clarisse Starling with decency, even affection.
We like our heroes to be a little "naughty," and our villains to be more "human."
It is a powerful technique to suddenly switch from the purely evil Monster, "Hannibal the Cannibal" to the erudite "Dr. Lecter."
All of the above plus the other characters (except for Clarisse) are never overly sympathetically portrayed, another trick to keep Lecter from becoming too overwhelmingly awful.
In the end I think it is all these things, plus as you noted, a masterful performance by Hopkins as well as a brilliant piece of work by the writers and directors!
(All in all, one of the all-time classic film "Greats!")
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