Gandalf wanted to use the eagles, he just didn't want anyone to know that was the plan incase Saruman would get word of it and counter the eagles. Unfortunately Gandalf fell with that balrog without being able to clearly tell the plan to Frodo and the others, instead he says "Fly, you fools" expecting them to understand all the while giving as less information as possible.
The entire reason for their long journey taking another path than the main path was especially to reach the eagles without saruman knowing about it.
That...Explains everything!