Hi Rick Casey,
The XAP minifier is suitable for small xap files (< 1MB), so if your project is bigger in size I would suggest you to use the Assembly Minifier. In the Assembly minifier you upload only Telerik Binaries so you don't have to worry about protecting your code - we're minifying only our code. And the reason that we need to do the minification at our side is that when we minify our own assemblies, we must sing them again with our private key and so on.
Please let us know if we can be of further help.
All the best,
the Telerik team