I actually made this question a couple of months ago and deleted it after a comment by Alexandre Eremenko, if I recall correctly, which, in my opinion, made it perfectly clear. I'll try to expand it a little:
It's used because of the word difference, whose latin etymology happens to start with a "d" also.
Differ comes from the latin word differre, derived from the word ferre which can often be translated by "carry". Pretty much every word which contains the word "differ" is derived from this.${}^*$ In here you can find a similar explanation of the etymology of the word.
From this it's clear that $\Delta$, $\delta$, $d$, and even $D$, are all associated with the change of a given quantity (except when talking about a river delta, in which case it has to do with how the greek uppercase symbol looks).
Even though this is most likely the reason, asking who was the first one to use it, or to set a bound would be very interesting. In that sense this isn't a complete answer.
$(*)$ I'm translating this from an etymological dictionary in spanish and assuming the roots can't be that different, given the overwhelming influence french had in it.