The President CAN NOT propose bills. And he can NOT veto sections of Bills. Congress writes the Bills and then loads them up with all kinds of extraneous expenses. If the President wants his budget for the Armed Forces, for instance, he frequently has to accept pork (a la bridges and roads and buildings named for Sen. Byrd of W. VA). Since all of the Senators and Congressmen like to bring home the bacon for their own districts the appropriations quickly fly out of control.
Did you see the President's request last week asking Congress to freeze all expenditures at 1%-2% over last year for everything, except National Defense? That's a good start, if Congress will go along with it. They won't, however, and the President can do nothing about it without a line item veto.