The rubber (when new) is actually a seal. It has a lip on each side which seals against the glass on one side and the body on the other. You're not going to be able to really fix it. Pull it check for rust underneath, make sure the windows are still well sealed and then either paint it black again, reinstall (with new clips) and then seal as best you can with some silicone or try to find replacements in the best shape possible.... Sadly most of those parts are no longer available new from Toyota so you have to make the best with what you have. The seal on the trim around the windshield is probably the most critical one and is responsible for about half of the wet headliners and rust along the windshield out there (on hard top models it's about 90%).
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