Learn Spanish (Spain): No es que sea descortés, sino que nadie le enseñó modales. - It's not that he's impolite, but that nobody taught him manners.

The phrase no es que (it's not that) is used to reject or deny a reason, which always triggers the subjunctive in Spanish. You are stating that his being impolite is not the true cause, so sea is required.

Why does the sentence use sino que for "but" instead of pero?

Sino is used for contrast to correct a negative statement, translating to "not A, but rather B". Because the second part of the sentence (nadie le enseñó modales) introduces a new conjugated verb (enseñó), you must use sino que instead of just sino.

If the first clause uses the subjunctive (sea), why doesn't the second clause (enseñó) use it too?

The second clause states the actual reason, which the speaker is declaring as a true fact. While the rejected reason after no es que takes the subjunctive, the affirmed reason that follows sino que takes the indicative.

Why is the pronoun le used here for "him" rather than lo?

In Spanish, you teach a subject or thing (the direct object) to a person (the indirect object). Here, the direct object is modales (manners). The person receiving the teaching is the indirect object, which requires the pronoun le.