I'm all for crate feeding. The crate needs to be associated with something 'good'.
Kipawa was doing the whining when we first crated him. He did not settle down. As Dmey mentioned, I would not let him out until he had settled down. Now, after feeding, I leave the crate door open with a few good toys in it. Kipawa is choosing to go into the crate on his own during the day to play with the toys.
If I have to leave the house, even with my husband at home, we crate Kipawa, as Kipawa moves tons faster than my hubby in his wheelchair :). Darrel tells me that Kipawa whines for about 10 solid minutes, then settles down and naps, then whines again, then settles down…. This repeats itself until I get home.
Then, when I let him out of his crate, he 'complains' to me - lots of talking and telling me he didn't like me leaving him. He is extremely attached to me, and we have to work on him being comfortable when I go out to get groceries, go to the pet store, etc.
Just remain consistent with what you do. Don't give in. Barring damaging himself in his crate, it's kind of like 'who will give in first'. I'm sure things will improve for you.