News Flash...
...if you hit a tom head, it will dent, no matter how softly you hit it (unless you *tap* it), if you hit a bass drum head with a hard beater, it will dent, bass drum heads need to be replaced too. Patches alter the sound too much, so much that on a recording it sounds like a completely different drum.
I'm not trying to sound like a jerk, I've worked as a studio drummer and as a studio drum supplier for about nine years in Nashville, Dallas, KC, Oklahoma City, Austin, etc... just replace the head more often if you like the beater. If you can't afford to do that, switch back to a softer beater.
Also as MadAudio said, look at your technique, don't bury it.