When you apply the brakes, the friction between the brake pads and the brake rotors causes the car to decelerate. This deceleration is due to the net force on the car, which is the vector sum of all the forces acting on the car.
In this case, the net force is the vector sum of the force of friction and the force of inertia. The force of friction is directed opposite to the direction of motion of the car, while the force of inertia is directed in the direction of motion of the car.
Since the force of friction is greater than the force of inertia, the net force on the car is negative. This means that the car is decelerating.
Therefore, the force is not balanced when you apply the brakes in a car.