Be Careful!
It sounds like you've been with this company for awhile so leaving for another job isn't as easy as it sounds. Starting with a new company means finding a good company with decent benefits, flex time, and overall good working environment. You might find yourself working for a similar type of manager. I think being upfront and honest is the best policy. Let him know your concerns. If the two of you just can't see eye-to-eye then looking for a new job might be the right answer. Just be careful! The economy in your area of the country may not be promoting a move at this time.