Ever spent some time alone at home and been spooked by weird noises? Multiply that by a thousand, and you'll get what Matt goes through when he's imprisoned at age seven by the possibly deranged, crazy Rosa. But that sort of real, physical isolation isn't the only kind the The House of the Scorpion deals with. Matt experiences what we might compare to the isolation of going to a new school, walking into the cafeteria and not knowing anyone or having a place to sit. Except instead of being an average student, Matt's a clone. And instead of going to school, he's joining his drug lord clone-daddy's household, where he is promptly shunned by his various relations. Same thing, really. At any rate, Matt isn't the only character who suffers from loneliness. Tam Lin is far from his home and trapped in service to El Patrón. The Lost Boys have all lost their families. Even Tom is isolated by his status as an illegitimate child. The harsh world Matt experiences, both in Opium and in Aztlán, isolates a lot of people and traps them in bad situations. So the fact that characters like Matt manage to make connections and cobble together a family is pretty remarkable.
Matt is often depicted as a very isolated and even lonely character, which makes his eventual ascent to leadership fitting – it is lonely at the top, after all.
El Patrón has effectively isolated himself from any sort of meaningful human contact; though he's a very bad man, his life is quite sad.