How should I be kind to my atheist father?

Allah, The Exalted, has decreed and ordained his slaves to be kind with parents, even if they are polytheists, by honoring and obeying them in all that isn`t sinful, so that they might love Islam and embrace it as a result.

Is it permissible for a mother to stop her daughter from marrying a respectable, God-fearing young man because he isn't college/university graduate?

It is impermissible to deny a woman her right in getting married except for a lawful reason, and problems can be solved through dialogue. However, she can file a suit in order for the judge to have a say in that regard.

Was Prophet Jesus (Peace be upon him) baptized?

Is it permissible for the guardian, or the father of the child to hit the latter in order to teach him/her good manners?

It is permissible for the guardian to hit his/her child for teaching them good manners once they become ten years old provided that it is done mildly, harmlessly and without intimidation. Actually, such punishment is to be employed gradually i.e. after: asking, warning, and scolding. As for the teacher, he isn`t allowed to hit the student unless the latter`s father approves of it, and it is done according to necessity without intimidation, or harm.