Why do you think Jane is more comfortable with Mr.Rochester when he is rude to her?
Ironically, when Mr. Rochester is rude to Jane, he is treating her as an equal and, in a sense, giving her the right to respond as an equal. He appreciates and enjoys her honesty, partly because he is honest himself. He is a "no-nonsense" sort of person, and he enjoys seeing that same quality reflected back at him in Jane. Their discussions are often quite humorous for this reason.
In a sense, Jane is a character who finds it easier to respond to rudeness than she does gentleness. What she likes about Rochester and the way that they interact is that it gives her the opportunity to speak the truth and not feel confined by social niceties and expectations. This is something that she has always struggled with. Rochester gives her the chance to be herself.
Rudeness is familiar to Jane; kindness is not. Ironically, people can be more comfortable with negative situations if there is a familiarity to them. And, although she is not the equal of Mr. Rochester, his stepping out of bounds allows her to do so, too.
Jane and Mr Rochester are not on an equal footing as far as 19th century society is concerned. He is a gentleman and landowner while she is the governess to his niece. As has been pointed out above, the rudeness allows Jane equality in their conversations. You need to consider social conventions of the day and that a single man and woman had to be careful about expressing themselves in an intimate manner because of the strict moral codes of Victorian England (which were largely hypocritical). I believe that Jane would have been uncomfortable with kindness, not just because she was unaccustomed to it, but because it could lead to a more intimate relationship with which she was ill-equipped to cope and which may not have been looked upon favourably by society. Jane is not free to form an intimate attachment to Rochester until after her status is improved and he is rendered less attractive following the fire at Thornfield. Therefore, rudeness provides a buffer between them that is actually to be welcomed.