The problem is that it isn't preinstalled, while iMessage and Facetime are.
Apple tries very hard to convince its users that its practices are not the problem, but those who choose not to use Apple products. Anything that doesn't come preinstalled is seen as an unnecessary inconvenience by most iPhone users.
No, they just prefer what iOS provides, or they don't know many people who use WhatsApp. For all it's popularity elsewhere, here in the States, WhatsApp is not used very much.
I've never downloaded WhatsApp, mainly because I don't know anyone who's on it. That's a bigger barrier than anything being preinstalled.