We'll, Tom might be not the most decent cat out there, he might be bad and insecure. One can even argue that he is a bad cat. But here we're trying to argue that Jerry is good regardless of who Tom is. It definitely can be that both Tom and Jerry are bad or both good. Jerry being good doesn't necessarily entail Tom being bad and vice versa.

I don't think that your argument about Jerry's nature is valid. Using the same logic one can argue that it is in the nature of kleptomaniacs to steal and therefore they have to be allowed to steal. Hence, Jerry is immoral, he parasitizes on Tom's owners instead of pursuing a less parasitic but more challenging existence like being a dampster rat where he can feed on what's been already thrown out.

No matter how mean Tom's owners are, Jerry is still the culprit for them, not Tom. They basically pay Tom to get rid of culprits like Jerry. Whether Tom is efficient at his job or whether he wreaks too much havoc by doing his job is a separate question and it doesn't absolve Jerry of his sins. 

Another nasty thing about Jerry is that he knows that Tom is insecure and he preys upon Tom's weaknesses while definitely enjoying the process.