“Dear” has been the conventional greeting in letters for centuries, and does not in that context bear any implication of affection or intimacy. For instance, you might very well write:
Dear Cable Company:
I have told your service rep several times that I am moving. Would you please come collect your box and put it where the sun doesn't shine?
“Hi” has largely replaced “Dear” in emails, because it is markedly less formal; but those of whose experience stretches back to manuscript are somewhat uncomfortable with this, and apt to revert to “Dear”. Your professor is likely to have put down “Dear” without thought; if he is deliberately signalling anything, it is just as likely to be a greater degree of formality (for instance, if he is warning you about your grades, or inviting you to apply for a scholarship).
So I would not worry about this, unless it is accompanied by other changes in his behavior towards you.