Not a historian, per se, but I am Albanian so I'd like to think I know enough on the topic to be able to discuss this here.

Although nobody likes to be governed by outside forces, from what I have come to understand, the Albanians were actually treated fairly well under Ottoman rule. As was the Ottoman policy, they either had to convert or pay tithes in order to keep their religion, and many chose to convert. Thus, a high volume of Albanians were taken into Anatolia where they either became janissaries or better, including Skanderbeg, Albania's national hero (Skanderbeg, however, would lead a revolt against the Ottomans under the name of Christianity).

The northern tribes (where I am from and predominantly in present-day Montenegro) famously refused to convert or pay taxes, and led successful battles against the Ottomans, with Ded Gjo Luli becoming the face of the revolution. Much of this history was recounted by Albanian priest Gjergj Fishta in his book, "The Highland Lute," written in the early part of the 20th century.

Still, the Ottomans were viewed as fair. One story goes as such: Cun Mula Juncaj, "bajraktar" (lit. "flag-bearer," akin to a tribal leader) of Hoti (one of the main Northern tribes) was told to convert to Islam. He struck a deal with the empire that if he himself converted, the rest of his tribe and family could retain their Catholicism without any consequences. They agreed, and thus, to this day, his original family name, Juncaj, remains Catholic, while his direct descendants took his primary name as their new family name, Cunmulaj, and are Muslim.