There’s a trope involving disgruntled people throwing tomatoes at people, such as bad comedians and people in stocks. Was this a common thing to happen? And why tomatoes?

Aimed throwing has been observed non-human primates, notably chimpanzees and others apes (more rarely monkeys). Throwing faeces, wet chow and other objects is usually done in the context of agonistic encounters. In some cases, it demonstrates planning abilities, as chimps are known to store rocks or faeces with the express purpose of flinging them later. It has been hypothetised that the refinement of neural architecture necessary to throw poo (and other things) has eventually supported other complex motor actions, including language and speech (Hopkins et al., 2012).

So: people who throw stuff at other people because they don't like them express million-year old abilities that predate Homo sapiens and that have helped hominids to hunt game and fight competing groups or individuals. Throwing tomatoes at comedians is just a late instance of this.

For now, I'll restrict the perimeter to tomato-throwing in theatres. I'll let specialists of classical Greek and Roman theatre tell you how common pelting actors with food items was in their period of study. One historian, Paulette Ghiron-Bistagned claimed that fourth-century Greek audiences assaulted actors with "various projectiles, tomatoes and eggs naturally, but also with any food that spectactors carried with them" (Ghiron-Bistagne, 1976). But the tomatoes, of course, are anachronistic... For Csapo and Slater (1995)

the slightest awkwardness could result in outbursts of disapproval, shouting, hissing (or whistling), clucking, heel banging, and, possibly, food throwing.

The latter is based on an ambiguous text of Demosthenes (On the crown) and it thus remains hypothetical that the actor had "figs, grapes, and olives" thrown at him. Still, public disturbances could result in the actors and chorus abandoning the performance. A special force of theater police, called "rod holders", has been mentioned.

Roman audiences were not much politer, shouting, hissing, insulting and booing actors - sometimes for just "reciting a verse that is one syllable too long or short" (Cicero, Stoic Paradoxes 3.26) and forcing plays to be terminated. Caspo and Salter do not mention food throwing though.

If we skip a few centuries and look at European theatre in the 17th century, let's say that actors had it rough. I've addressed in a previous answer the question of violence in theatre in the modern era. Theatres were hardly the quiet and polite places that we are familiar with: people brought drinks and food and were generally noisy and unruly, while theatres were homes to vendors, cutpurses, and prostitutes.

British author Jean Gailhard, visiting Venice in the mid-1600s, reported:

In point of Playes, that which is the most Comical, is that whereat Venetians are pleased best of all, and indeed their Bouffoons go beyond any in the world; and if the young Nobles who stand by be not pleased at what is acted, sometime out of frolick, they hiss, whistle, throw Apples and other things upon the Actors, and do such like things, which if it were not in Carnaval time, were much unbecoming the Venetian Gravity.

In France, 17th century theatres were very lively places - in the mid-1600s some privileged spectators were seated on the stage itself! The lower seating area reserved for the common audience, the parterre, was described by some authors in animalistic terms. Violence was recurrent. In 1672, a performance by Molière's troupe had to be interrupted twice, the first time because someone in the parterre had thrown an object, "the large end of a smoking pipe", at the actors, and the second time because a man was beating another with a stick (Ravel, 1999).

More policing, and the creation of the state-run Comédie-Française resulted in a more civil behavour, though incidents still happened: in 1691 a captain named Sallo, accompanied by other soldiers, threatened to shoot the actors and to run the employees through his sword, and he and his men proceeded to destroy the theatre. In the 18th century, a forceful policing system was put in place - soldiers were put in theatres, as well as spies (mouches) who surveyed the troublemakers in the audience. This policing was not without problems as it was prone to abuse and to the occasional shooting, but it seems to have made French theatres more "civilised" (Ravel, 1999). In 1776, a British tourist in Paris was impressed by the good behaviour of French spectators compared to that of his countrymen:

During the representations here, the attention of the house is remarkable; there is no whistling between the fingers, no bawling for roast beef, nor pelting the parterre with oranges, but the public behaviour is such, as becomes those who lay claim to the title of a polished people. Upon the whole, our theatre, when compared to that of Paris, is little better than a bear-garden ; and I have no expectation (whatever account our own vanity may make of it) that it will ever bear any reputation among foreigners, before its regulation be totally altered, and no such glaring vestiges of le barbarism remain.

Not everyone agreed. In 1787, an anonymous French author, E.M.L, wrote a pamphlet where he claimed that theatre policing though terror and bayonets was less efficient to keep people in line than the oranges, onions, and apples thrown in the self-regulating English stages. That year, members of the parterre pelted with oranges the Marquis de Gouy d'Arsy, who had placed his chair on stage and blocked the view of parterre spectators (Ravel, 1999).

Oranges, indeed, seem to have been at that time the preferred projectile of European audiences. A French troupe performing in London in 1752 was attacked twice by spectators throwing orange peels, but the second time ended tragically when defenders of the Frenchmen responded with swords (Anonymous, 1797; note that I haven't found confirmation of this incident). Oranges are also mentioned in 1770 when they were used to cancel a play titled The Brave Irishman in London (the culprits were personal enemies of the author) (Rousseau, 1770).

Louis Simond, a Frenchman travelling in 1810-1811 in Great Britain, tells that the upper balcony of the London Opera (the "paradise" or "the gods"), occupied by the populace, threw "bits of apples, nut shells, oranges peels etc." on the actors and on the spectators below them (Simond, 1816).

In 19th century France, the dominant fruit used as a projectile in theatre was the apple. It is mentioned for instance in 1831 in La France Nouvelle: after a troupe had refused to perform a play demanded by the audience, they were pelted with apples and onions (La France Nouvelle, 8 February 1831). In 1833, a vagrant arrested by the Parisian police was asked about his occupation: he answered that he was employé aux trognons de pommes - an "apple cores employee" - by the theatre Les Folies-Dramatiques, and paid 15 sous by night to prevent spectators from throwing apple cores from the upper balcony. The story amused caricaturists and humorists for years (Berthier, 1994). According to Pougin, apples were preferably cooked (pommes cuites): a talentless actor could be said to be "bad enough to have cooked apples thrown at him" (Pougin, 1885).

The public could be creative when it came to projectiles: the first and controversial appearance of courtisan Jane Harding as a singer at the Opéra-Comique in 1894 was welcomed with "carots, string beans, a live rabbit with a pink ribbon on its neck, a codfish, and calf's lights (mou de veau) (La Petite Gironde, 25 February 1894).

->Continued: But what about tomatoes?