I was about to say, "Never realised that", but it seems to ring a bell now.
Messenger is so strongly associated with FB having become the mobile phone version of their personal messaging function, and as far as I know you can only use it to message people who have a FB account (whether or not they are your FB friend). However, in view of
@Sandra6 's post that seems to be different now and Messenger will probably have the same functionality as Whatsapp as well as also being independent of FB. You can already set Messenger as a means to show your text messages but I disabled that because every time I got a text it was duplicated via Messenger.
What I like about Whatsapp is that you can use it to communicate with any other mobile phone if the owner has the Whatsapp app on their device. Photos and files can be sent free whereas they convert texts from SMS to MMS thus incurring charges, and a lengthy text doesn't convert an SMS to MMS as it does on my mobile phone, so it is always free.
If Messenger can now be used as a standalone, I doubt Facebook will get rid of Whatsapp as it seems it allows them to cover all angles by Facebook providing an app for people who don;t like Facebook.