I was in exactly the same situation - a faculty member who had a travel consulting business on the side. Several things - first, for a simple domestic trip, $50/leg is way out of the ballpark for the going rate. I charge $35 for a domestic roundtrip and $50 for an international one. If there are other requirements, you can add on.
Second, and maybe even more important, many universities, especially public ones, have conflict of interest rules that are very strict. As an employee of the universiity, you may be forbidden from charging a fee to another university employee. The university looks at such transactions as giving you, the employee, unfair advantage over non-university travel agents in obtaining the business of another university employee. Be sure to check with your accounting dept or HR dept before you start.