That's what it really comes down to. From what I can see, it's mostly an emotional response. I'd be surprised if code/binary obfuscation is a net win in general.
I've had to disabuse developers of this idea. One distributed binaries that weren't quite valid but ran on the CLR, though not Mono. A 10 line script was enough to remove the invalid sequences. What did the developer gain in this case? An extra build step, undoubtedly more than one bug, and in the end, no "protection".