Ha, no it's not. Any game that gains popularity is not protected (I mean really... Spore, anyone?), and any game that doesn't gain popularity isn't worth overcomplicating in the name of unnecessary and ineffective protection. And I highly doubt media licenses would seriously force me to deliver them in a "protected" pack file (I could be wrong, but I'd be surprised)... The reason I listed "(Slightly) harder for users to muck with" as a pro is not so much because it would stop Average Joe from replacing a texture (because if Pro-Hacker Henry hacks the file anyway, all he needs to do is release a program and Average Joe can now do everything Pro-Hacker Henry can do), but because I think some modders get a kick out of reverse engineering things and in a way it helps develop a modding community for the game, which (if done correctly) I think can be a good thing. [edit: Hodgman has pointed out that this has come across as quite arrogant; please read my post below, as that was not my intention (and realize I am not talking about the legal issues of fulfilling a contract here; I'm talking more about what frob said above)]
An other point is, that many third party resources (textures,sounds,models etc.) are coming with a license which forces you to deliver the resources in a protected way. A resource file(!=simple zip) is atleast a basic protection.
Anyway, sorry, I'm not trying to start a holy war here. You've all brought up some great points. I hadn't thought about anti-virus programs, and I didn't realize Windows struggled with lots of files in one folder (I'd probably categorize them in subfolders anyway, but it's good to know).