I have a 24 year old son, an 11 year old daughter and a 6 year old son. My 24 year old was always healthy and fit when he lived at home and was really good about eating whatever I made for him and had a really good appetite for healthy foods. Unfortunately, he has gained around 50 pounds since he moved out of the house almost 3 years ago. I believe the reason why is two-fold...1) the people he lives with now fry everything and eat a very unhealthy diet, and he eats what they eat. 2) I never trained him to shop for and cook with healthy foods. Sure, that's what I kept in the house for him, and I still do it now with my younger kids, but not really having him involved in the shopping and preparation of the food didn't give him the long-term skills he needed to stay healthy after leaving home. It's great that you're concerned about your son's diet, but I just wanted to say that it's going to be a process that will require more than just providing him with healthy foods at home. He needs to be really educated about what is healthy, why it's healthy, and how to maintain his health when he's having to provide for himself.
Now, contrary to some other moms here, I think that the foods you mention your son likes aren't all that bad. There is some nutritional value in almost every food. Cheese - calcium, pasta - iron, beans - fiber, chicken - protein, chocolate milk - calcium and anti-oxidents, etc., etc. If he doesn't like veggies, fruit is a viable substitute. As long as he's eating a good balance of nutrients, eating a reasonable number of calories on a daily basis, and getting at least 30 minutes of some sort of physical activity most days of the week, he will probably be ok.
To help the process, you might start buying whole wheat pasta and tortillas. I know there are some boxed mac & cheese brands that are whole wheat now. Buy the lower fat cheeses. Brown instead of white rice. Make your own homemade pinto beans and mash them up with a little fat free low sodium chicken broth/stock to make them "mock refried" beans so that there is no lard involved. Always keep fruits and the healthy snacks that you do know he likes on hand. If he likes chicken, how does he feel about turkey? Limit the QUANTITY of the higher fat and calorie foods (pasta & parmesan, mac & cheese, etc.) and supplement with lower fat/cal foods like fruits. I don't think there's anything wrong with a small bowl (cup or so) of mac & cheese, some baked chicken and an apple or pear for dinner. If that doesn't fill him up, let him have another piece of chicken or another piece of fruit, but not more mac & cheese.
I don't think it is wise for you to just let him have what he wants rather than what you fix for yourself all the time. Make him at least taste what you're making for the family and if he doesn't like it, then he can have some other HEALTHY alternative like fruits, veggies, lean meats, whole grain breads/snacks, etc. It's always best to pair a protein with a carb rather than just have a carb by itself, but once in a while is not a big deal.
My 6 year old is very picky and also underweight so I worry about his diet quite a bit. A counselor told me that I should require that he taste everything on his plate before he can finish and that he will get used to eating the things he "thinks" he doesn't like. She said he will eventually do it on his own and if he makes it a habit to always at least taste what's put in front of him, he will find more and more things he really likes over time. We've been doing this now since he was 4 and while he's still picky, he's gotten better especially when it comes to vegetables. Maybe this could work for your son too. Good luck!
Blessings,
N.