I took off my rear wheel last night and realized my tire has been rubbing my frame on the inside of the left seat stay, right under the rear brake caliper. My wheel looks to be sitting in there straight and was recently trued.

First of all I can't figure out why it's happening and second of all is there anything I can put on the frame to protect it?

The first thing I would check is the skewer. If it's not tight, your wheel may pull loose.

The wheel might be out of dish too. That's what happened with mine after it was trued.

Skewer is/was fine. Out of dish, does that mean its pulled towards one side? The wheel lines up fine when set in the frame.

So you can see marks on the frame but as the wheel sits now the tire isn't touching or close to touching? How bad are the marks, does it seem like its been going for a long time or could it have been the wheel being crooked in the dropouts for one ride?

This would be my suspicion.

rubbing is bad. If you can't figure out the cause, take it to the LBS. You don't want to continue this way.