What does Hemingway mean when he says "But, thank God, they are not as intelligent as we who kill them; although they are more noble and able."in...

Santiago in Hemingway's The Old Man and the
Sea demonstrates a great respect for the fish that are, in effect, his foes. 
He respects and in a sense loves the fish, though he catches them, or tries to, in order
to stay alive himself. 

In the quote you ask about,
Santiago is grateful that fishermen are smarter than fish.  Humans, of course, have a
higher level of intelligence than fish.  This enables someone like Santiago to use tools
to catch them.  Otherwise, Santiago would have no hope of competing with a
marlin.

Yet, these huge creatures (marlins) are in some
ways more noble than humans.  They are far superior in strength, of course, and the
marlin Santiago fights with matches his endurance minute by minute and hour by hour. 
The fish is a creature who roams freely in its natural environment and is part of the
natural world that Santiago respects and admires.  The novel comes down to a test of
wills between the fish and Santiago, and though the fisherman wins, it is a great
struggle and Santiago wins at great physical costs. 

In
fact, it takes a man like Santiago, who shows nobility himself, to defeat the noble and
able creature.