I think Malcolm X was an important historical figure, but was good more in the generic than the specific. Nation of Islam, as an organisation, provided a myth to justify violent struggle against a society that systemically oppressed black people. That oppression, itself violent, justified a variety of stances against it, from the peaceful-direct-action of more mainstream groups to violent militarism. I have take little issue with the idea of violent resistance against racism (and offer a nuanced solidarity for groups that practice that today, like Anti-Racist Action). I do take issue with Nation of Islam specifically for two things: separatism and its own racism (the latter being more problematic). I don't believe separatism is healthy; it does not permit a culture to grow when it slices off bits of itself that it can't manage to relate to. I believe that the racism in Nation of Islam was deeply harmful in that it recreated the atrocities it faced, and perpetuated them by making peace impossible.
I recognise there is a difficult dynamic between oppressed and oppressor peoples once the systemic (and often literal) violence of the oppressor is met by literal violence of the oppressed. The oppressed cannot be expected to simply be beaten, nor can the oppressor easily stop once it is being struck back. Drawing down of tensions is a difficult process (as the Israeli-Palestinian conflict has shown when enough doves on each side were active).
Malcolm X's experiences in Mecca significantly redeemed him in the eyes of history; seeing the various races making Hajj together opened his eyes to the possibility of better goals than a separate existence. It is a great pity that he was killed not long after returning to the United States; his late writings about the universal solidarity of man are inspirational.
What I particularly like about his late politics is that it is not the foolhardy absolute pacifism that one often hears, but rather what strikes me as the sensible "I will insist on our common humanity, and if you trample me I will fuck you up even if I lose, but I am ready to extend my hand in equality and peace if you are". That, I think, is the way we should each approach the rest of society. Thorny and complicated, yes, but avoiding the wrongs of all the obvious simpler positions.
(I recognise that the reliance on faith and ritual for what I'd call his redemption is an inconvenient fact for a far-left atheist interested in social justice; I have no answer to that criticism but don't consider it more than a good jab)