Need advice on what to say to son after he was rejected from MIT, but a boy he tutors in math and science was accepted

Back to the OP.

Life is a long journey. Every one of us has experienced ups and downs along the way. When your son feels a bit down, the last thing he should do is to stop and dwell on it. Instead, direct his energy to accelerate and move past it as quickly as he can. A barrier can slow someone down, but it can also serve as an invaluable training for him to overcome many other (and likely higher) barriers that he will surely encounter along his journey.