Good to ask questions. I own an agency that does crisis and exotic vacations <think exotic locations not girls to be clear>.
If all you do is book simple air it'd be hard to justify $50 a leg which is more than most experienced agents would charge. Also the university likely would get upset at increased travel costs.
Good agents always use client cards to book with the travel partner. (Airline cruise etc). Thus booking on your card and charging him may not work and cuts some credit card protections off for him. Also you would end up eating credit card fees.
Doing TA work it not going to make you quick easy bucks.