Well, the source code is yours and unless you explicitly provide it, youll perobably only be providing compiled binaries.
Now, these compiled binaries are IL code. To prevent someone "decompiling" and reverse engineering your IL code back to source code, you'll need to obfuscate the IL code. This is done with a code obfuscator. There are many in the marketplace.
You've already done this with dotfuscator, however, you say that it only changed the function names, not all the source code. It sounds like you're using the dotfuscator edition that comes with Visual Studio. This is effectively the "community edition" and only contains a subset of the functionality of the "professional edition". Please see this link for a comparison matrix of the features of the community edition and the professional edition.
If you want more obfuscation of your code (specifically to protect against people using tools such as Reflector), you'll need the professional edition of Dotfuscator, or another code obfuscator product that contains similar functionality.