Why are the Democrats cowering to the Republicans in Congress when the Republicans do not have two-thirds vote?

The Democrats outnumber the Republicans in the Senate. They own the Executive Branch (the President is a Democrat). And they have enough numbers in the House of Representatives that the Republicans cannot get a two-thirds vote by themselves there. So why did the Democrats start acting helpless after the last election. (I know I'm missing something here; I would appreciate your enlightenment.)