Look at the greatest villains ever: Dexter Morgan, Lex Luthor, etc. Good writing should make you feel for the villain as much as for the hero, and make them seem like they have good intentions. Victor Fries falls into this category, with his suspended, dying wife and his unusual tragic condition. Even though he has good intentions, he frequently breaks the laws we have in place for selfish reasons. From industrial espionage to cold-blooded murder, he always seems to go back to his criminal ways. Other villains, such as Joker and Riddler, have also teamed up with Batman, but they follow the same pattern, returning to their law breaking ways.
Although Mr.Freeze has indeed done villainous things its all for his wife who is frozen because she has a disease and Victor (his real name) has done everything he can just to make sure the love of his life can at least live. He has also helped Batman and in some cases redeemed himself.