Trump can charge whomever he pleases rent to stay in his tower. He can charge secret service members to stay in his towers as long as there is nothing in the U.S. Constitution that bars such activities. Maybe he can comp them at a casino hotel, too. Anything is possible.
No, Trump should not charge rent to the Secret Service for space in the Trump Tower. The Secret Service is their as a service and should not be charged for the space. If Trump chooses to stay at Trump Tower, then he should provide space for those working to protect him.
The secret service provides Trump's security and they should be compensated accordingly. It is not proper to charge rent to people that provide a valuable service. Since Trump is not even taking a salary as President, it is extremely unlikely that he would charge the Secret Service for providing a service that is very much needed.
Trump shouldn't charge rent to the Secret Service, and the Secret Service shouldn't charge Trump for their services, either. Both are doing the job for the people that they were elected to do and they were hired to do. Their jobs are necessary. Each should accommodate the other without payments.