I had this problem with my old Windows Mobile phone if I was tethering and downloading torrents but I have not had this problem with the Pre at all.
Are you running the latest version of webOS?
When this happens take the back cover off feel the back is it the battery that is hot or is it just below the battery?
Are you running any homebrew apps?
Have you applied any patches (hacks) to your Pre?
Is this with a car charger, wall charger, or charging through a computer?
Is said charger an official Palm charger or 3rd party?
What were you running before this happened?
Can you replicate the issue by opening a certain app?
Does it do this while not plugged in as well?
What type of service do you have when this happens?
You said it happens on the car charger while using Sprint nav... are you driving in a rural area?
It sounds like you may have a program hanging and killing the CPU. I know this seems like a lot of questions but I can troubleshoot if you answer them
For now I recommend resetting the Pre when this happens like you have been doing. Just hold Orange button + Symbol + R you don't have to pull the battery.