Hello mate, it sounds as though you haven't assigned a button to the brakes in the controls menu. RAF planes don't have toe brakes, it's a lever on the joystick.
Go to 'options/controls', click the 'keys' tab, then in the 'category' drop down box click 'aircraft', then scroll down to 'full wheel brakes', and assign one of your joystick buttons to this function. Differential braking is achieved by using this button in conjunction with rudder.
Nice user friendly GUI, isn't it?