I suspect it's because WhatsApp's backend can be turned into a platform that will run WhatsApp itself as well as Facebook Messenger.

There's a lot more opportunity to do messaging between businesses and individuals (eg. customer service) as well -- see messenger for business.

Not saying Facebook isn't out to sell ads, just that there's probably a lot of reasons that Facebook might want WhatsApp's technology and team. Especially as they try to move more conversations onto their platform and reach out into other markets.