You can obfuscate the code (look

), so it's harder for the people who decompile your application to read (but not impossible, of course).
Maybe you can change the header or anything like this, so the decompilers don't accept your application as an AutoIt application. But for the programers of a decompiler it's easy to recover the header and decompile it.
So I think that there aren't any other ways to protect it. AutoIt is open source. Deal with it (I heard this from several people).