An insightful article in the International Herald Tribune today discussed the psychology behind booing and had an anecdote about Maestro Muti’s reaction to the loggione's antics.
In 2000 at Teatro alla Scala while Muti was conducting Il Trovatore, the loggionisti booed his [and ultimately Salvatore Licitra’s] interpretation after Act III. Muti responded to the booing by not ducking his head under the orchestra pit, but by turning towards the audience and saying, “The opera house is not a circus”. Muti responded to the sass…by turning-up the sass. He’s sassy.
UPDATE: David Patrick Stearns at the Philadelphia Inquirer wrote an article on Alagna's recent kerfuffle at La Scala. His vague theory behind the booing is a bit of a stretch for me, stating that the disapproving jeers stemmed from years of hatred that simmered...and finally exploded towards the Alagnas (basically, retribution for bad behavior and h8rs who are jealous).