The explanation I was given was that the binding energy of the quarks in a proton is greater than the energy it takes to create a new set of quarks. So before you can pump enough energy into a proton to split it, you've pumped enough energy in for new quarks to appear, and you end up with two particles but no naked quarks.

Back then scientists didn't have a model for what is inside an atom though, while we do have a model for what is inside a proton.

>Back then scientists didn't have a model for what is inside an atom though

Yes, they did:

http://en.wikipedia.org/wiki/Bohr_model

From 1913.

Not a complete model, as we now know, but nonetheless, scientists did have a model of the atom 100 years ago.

Gahh but that's not how quarks work. Paired up, always.