Noise starts from a clean state with modern knowledge of cryptography and modern cryptography. Much easier to understand and replicate, much harder to shoot yourself in the foot with.

TLS brings modularity and evolutivity, much needed in a protocol the scale of HTTP. In Whatsapp's case, Whatsapp controls both the server and the client; it is much easier to transition between versions because all bricks are under control. When you don't need what TLS brings anymore it makes sense to discard it.

As another example: Tarsnap (https://www.tarsnap.com/) uses spiped (https://www.tarsnap.com/spiped.html), a very simple yet powerful mechanism to build an encrypted channel. Its protocol and proof fit in ~100 lines (https://github.com/Tarsnap/spiped/blob/master/README). When you don't need all the jazz provided by TLS (and when you're lucky enough to be able to pre-share keys, which helps a lot) then a simple protocol is good.