He is worried about Michael's safety. With the Don out of action, Tom doesn't want anything to happen to the chosen one. After all, he and the Don had many talks on what the Don wanted for Michael and this was not one of them.

Remember, this is one time the Corleones were not running the show. The Turk was in control of what was to happen, where and when. It put them in a position that they really didn't like to be in. Any strong arm move and Michael would surely be the one to take the first hit. Fast and lose was not the way Vito played things. They were always thought out and well planned.
Tom knew this and he didn't like the feel of how things were going.