Cross fit focuses primarily on one. The frontal plane of motion. In other words, a lot of up and down and forward and backward. Yes, it has its place and one can gain strength and change their physique in a positive manner.
However, it really lacks in sagittal and transverse motions, the side to side and rotational movements.
Football obviously requires strength and abilities in each direction like any other sport. This is a big reason programs avoid cross fit. They may still use Olympic lifts, though Cross Fitters like to pretend Cross Fit invented the Olympic lift. Another issue is that a lot of Cross Fit focuses on quantity over quality resulting in a high injury rate. Some facilities do a great job, but it's a franchise and most facilities are a nearby physical therapist's dream.
In the end, Cross Fit really isn't overall very functional for anyone, but if done correctly, it's still better than ignoring health altogether.