Been watching the movie Young Frankenstein, where the audience throws various vegetables at the Monster when he gets freaked by the shorted-out light. Question of course is whether audiences ever did such things-I want to say it was during vaudeville’s heyday but it likely predates that (the meme anyway).
It predates vaudeville. Washington Irving in 1802 described audiences expressing displeasure by “stamping, hissing, roaring, whistling,” occasionally “groaning in cadence,” and throwing “apple, nuts, and ginger-bread” at the stage. (Letters of Jonathan Oldstyle, Gent.).
Theater audiences in the early 19th century were boisterous, loud, and unattentive. Protitutes plied their trade pretty openly in the balcony, audience membered routinely heckled the actors, the actors would drop character to comment on things happening in the audience, and people often paid more attention to others in the audience than in the performance.
Audiences quieted down by the end of the century, but the tradition had been established.
I would think that most food products, especially the nuts and prepared gingerbread would have been too expensive to just be wasted like this. Now, rotten produce I can kinda see. But gingerbread? 
They sold all those things to the audience, so I imagine it was a case of what they had on hand at the time.
I was only quoting a contemporaneous observer.
But it was more a matter of opportunity: they had brought the food to eat, but started throwing it to disapprove of the performance. If they were* planning* to boo the performance (which was a common occurance), then they would bring food they weren’t planning to eat.