Agreed. My youngest son wanted to play football in college. He played 6-man football in high school and could run the 40 in 3.9 seconds. He was a mediocre student, but willing to work hard. He did manage to get into a D2 school. He would have been fooling himself if he tried to go to one of the more famous D1 schools. So, there is a place for everyone if they are willing to look and not confine their choices.
Are you sure that you didn’t mean 40 in 4.9? 3.9 would be significantly faster than anyone who has been timed in the NFL.
If your son could run the 40 in 3.9, he could go directly to the NFL. Or the Olympics. That's a couple of tenths faster than the fastest NFL players.
You have to mean 4.9 seconds. If he runs 3.9 and can prove it, every d1 school in the country will want him.
Here is an article about the runner up Heisman trophy winner Mantei Teo
"Manti Te’o improves time on 40-yard dash at pro day By Xai Xiong March 27, 2013 After running 4.82 seconds in the 40-yard dash at the NFL combine, Manti Te’O improved his time with 4.75 and 4.71 seconds at Notre Dame’s pro day. “I felt good. I’m at home now,” Te’o said. “I was very pleased with how I performed.” With the time that Te’O received in the NFL combine, many teams were suddenly afraid to draft him in the first round of the NFL draft. "