This sort of scenario happens from time to time. Before a flight the crew will calculate the flap setting and speed at which the aircraft rotates based on aircraft weight, the weather conditions, and runway length. If any of these are entered incorrectly, the aircraft could rotate too soon and not lift off when expected.
To decrease wear on the engines, modern jet airliners will often use less than full takeoff thrust. If the crew finds the aircraft is not accelerating or lifting off as expected, they can increase the thrust to the full takeoff setting. This is probably the first thing to check as it's a quick and easy step that would help get the aircraft up to the necessary speed and in the air faster.
It's very unlikely that a crew would decrease flaps in this situation, as this would decrease the lift, and thus take even longer for the aircraft to lift off. There have been several crashes where insufficient flaps were suspected as a contributing factor, causing the airplane to not lift off as expected and making it more difficult to control at low speeds. The crew might actually increase flaps to lower the speed needed to lift off.
The crew may also decide to to reject the takeoff. By the time an aircraft is rotating, there may not be enough runway left to stop safely, so the crew must make a quick decision as to what the safest option is.