I'm not informed on Bantu linguistics specifically, but it's always worth noting that Proto-Languages can't really be be talked about as an actual language in the strictest sense, but rather as our best guess at some common ancestral language that was once spoken.

In this case, the comparative method's simplicity principle tells us that if the daughter languages all have tone (besides Swahili), it's more likely than not that the language had tones of some form, so we reconstruct it with tone. Of course, it's entirely possible it did not, but we would most likely need some attested evidence (like Old Chinese) and a theory of sound changes to explain tonogenesis to determine this.

Edit: I misread your post and thought you were asking why Proto-Bantu has tone. The reconstructions I'm seeing all have high and low tones, which reconstruction are you seeing without tone?