It's very similar to that song about how all the bones are connected.
Simply: running gear connected to gearbox which is connected to engine. In-gear you have a link with no slack. Simply put, you can force the engine to reduce revolutions (i.e. braking in-gear) rather than let it reduce on its own (neutral, no accelerator). This means that you're providing a moment opposite to that which the engine is generating through its natural rotation. Since the crank shaft is connected directly to the cam belt (and a whole assortment of other belts) and the gearbox applies this force on the crank shaft, you have a situation where you're effectively pulling it the other way due to the rotational inertia already present in the cam shaft, crank shaft, etc.
In simpler terms, it's equivalent to stopping a free-wheeling tyre of an upside-down bicycle with your hands rather than letting it slow to a stop due to resistance.