A full 747 is a very profitable bird.
The problem is using 747 on markets that do not justify them. In 2010 the 747s were packed to Europe. Today, competition from ME airlines (although HK managed to keep EY out of HKIA) and the European crisis mean that the 747s are not that profitable on many routes where they cannot be filled.
And as Cathay Boy mentions, they are old birds, so a little bit more expensive to maintain. But on an old bird, most of the parts have been replaced, sometimes many times, so the argument should not be overemphasized.