The MD-11 is popular as a freighter because there's really no competition for it in the freight market. On the passenger side, the 777 now makes the MD-11 completely obsolete, but it will be a while before any cargo version of the 777 comes out. The MD-11 isn't the most efficient passenger plane, but it still is the most efficient freighter.
If your company doesn't do enough business to require huge 747 freighters, what are the alternatives? The A340 would could never make a good freighter, and the 777 is the only other plane around that can fly the very-long routes. The 767 is a successful frieghter, but it can't fly the Pacific like the MD-11 can.