This is an easy root method for the HTC Thunderbolt. While I say easy it is a long process but easy just the same. This method has only been tested on the HTC Thunderbolt with firmware versions 1.12.605.9 and below (just keep this in mind before you start).
Rooting instructions for the HTC Thunderbolt
Put your phone in USB Debugging Mode (settings -> applications -> development -> Click USB Debugging)
Turn off WiFi and plug your phone into your computer
Click step 1 … the program will say starting daemon, find your device and then start pushing files (be patient this can take up to 10 minutes)
Your phone will restart when this is complete (if not close rooter.exe, restart it and click step 1 again)
After your phone restarts it will come up to your boot system screen (Bootloader will be highlighted in blue)
Make sure Bootloader is selected and hit your power button (this will take a minute and go through checking PG05IMG.zip)
Your phone will ask if you want to update, press Volume Up
Your Phone will begin updating (when done it will say Update complete.
Press Power to reboot your phone
Your phone will boot to the main screen (skip the phones setup)
Turn USB Debugging mode back on again and unplug and re-plug your phone back into the computer.
Click step 2 … (if your phone comes up with an error close rooter.exe and restart it and click step 2 again)
The program will start pushing files to your phone (when complete your phone will reboot into the system menu again)
Top of your screen will say MECHA XD ENG S-OFF and bootloader will be highlighted in blue again.
Make sure bootloader is selected and press your power button (it will take a minute checking the PG05IMG.zip file)
It will ask you again if you want to upgrade (press volume up and the phone will start updating)
When complete it will say Update complete … Press Power to reboot your phone. (if it boots into clockwork recovery just reboot again into the main system)
Skip through the setup options again, turn USB Debugging back on and unplug and re-plug your phone back in.
Click step 3 … (your phone will sit for a while be patient its doing things, when done your phone will reboot)
If your phone didn’t reboot when completed close rooter.exe, restart it, and click step 3 again
Enjoy your Rooted Thunderbolt
As always Android Advice takes no responsibility for use of these instructions as they are here for those of you that already have some idea of what your doing and know that this may void your phones warranty.
Credit for the Rooter.zip can be found at: http://forum.xda-developers.com/showthread.php?t=1005292