They throw out far more than that in unsold food at the end of the day.

Again, if the store is wasting food, boycott it (or persuade it to stop doing so).

Decent coffee shops partner with local homeless shelters, or food apps / messageboards (Olio, Too Good To Go, …), to find takers for their leftovers.

It’s not really about the cost of the cup.

Indeed, which is why I did not say that it was “really about the cost of the cup”. The latter is, as you correctly imply, only one factor.