According to Merriam-Webster:
make, verb, definition 15 a :
to conclude as to the nature or meaning of something
We ask, "What do you make of it?" when we are deeply confused or baffled by something. Some examples of situations where you might ask this question:
- you find a strange coin and bring it to an expert coin collector to assess
- you can't read your doctor's horrible handwriting and ask someone else to help you
- your spouse's ex, whom you do not get along with, sends you a sweet birthday card out of the blue, and you want your spouse's opinion
"What do you think of it?" is a broad question asking generally someone's opinion. It could include all of the above situations, but is not at all limited to that type of question.