TextMate newbie here.
I hate to have to grab my mouse to click that Regular Expressions box nearly every time I search.
EDIT: the Regex check box becomes unchecked anytime after using ⌘-F in Safari.
Do you have the latest version of TextMate? On mine it remembers across launches/reboots. Go to TextMate -> Preferences, then Software Update. Under Watch For: select Cutting-Edge. Then select Check Now and install the update.