as we all know transformers are able to re-enter the earths atmosphere without burning up however i always wonder what would happen if they were damaged while entering the earths atmosphere. for example optimus is damaged and his circuitry and other inside machinery are sticking out so i wonder would he burn up since his robotic parts that are not protected from his armour burn up and then continue to burn him from the inside out?

If you look at the prequel comic, we see something of an answer to this.

Megatron is chasing the Allspark and has come to Earth. He has the coordinates of it's exact location as well, due to it's homing beacon that it emits. Upon entry into the atmosphere, and because he's not in a mode suitable for re-entry (the Autobots in the movie if you watch are covered with something that peels off as they're entering the atmosphere). This causes him to wind up far off course and land in the Arctic. His heated body touching the ice melts the ice and he plummets through to the icy cold water beneath. His body still very hot suddently cooled at the immediate pace that it was, is what led him to be frozen and stuck in stasis and lost until Capt. Witwicky found him.

As for whether it damaged him internally, no. It didn't do anything save for screwing up his telemetry and losing the homing signal of the Allspark.

So no. Prime wouldn't have been damaged, but he definitely would have been probably thrown off course and landed somewhere else than originally intended.

Megatron's alt mode was designed for space travel, Optimus Prime's was not. In the movie, they speculate that Earth's magnetic field threw off Megatron's navigation, not any damage from entering the atmosphere. Optimus Prime would probably sustain serious damage upon entering the atmosphere if his shielding was damaged beforehand.

Yes, his alt mode was designed for SPACE travel, but reentry into an atmosphere such as ours may not have been a part of the original design. Don't forget, they know nothing of Earth when the Allspark was launched from their planet. So reentry designs may have been built with Cybertron in mind and a couple of planets with an atmosphere of similar structure. They went with designs with what they knew. You can't build something with intent to work on something you don't even know exists.

Here's what Megatron narrates to the reader in the prequel comic, and this is the entry on his approach to Earth to his shut down and entrapment in the ice:

when i say parts i mean like say if optimus head was ripped open partly so his data bank or memory core thing in his head was showing which to us is a brain then wouldnt the heat burn his brains out?

Depens on what his "brains" are made of.

ok thanks