All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
It is not permissible for him to take that money for himself; rather, he should give it to his employer unless he was given permission by his employer to take it and to charge his clients extra money. He is but a Wakeel [an agent] who deals with the clients on behalf of the travel agency.
Indeed, the scholars stated that if the Wakeel charges the clients extra money than what was determined for him to charge them, then this extra money is for the Muwakkil [the person who deputized him, i.e. the employer] and not for him.
Allaah Knows best.