From wikipedia (because I am lazy):

The bunny hop is executed by approaching an obstacle with a medium rolling speed, arms and legs slightly bent. Upon reaching the obstacle, the rider first needs to shift their center of gravity towards the rear wheel of the bike and pull back on the handlebars, causing the front wheel to lift as if doing a manual. As the front wheel reaches maximum height, they 'scoop' up the rear of the bike by pointing their toes downwards and applying backwards and upwards force to the pedals, while pushing down and forward on the handlebars. It helps to think about the lifting of the back tire as snapping one's wrist forward and shifting their weight at the same time. The combination of these two motions allows the rider to first raise their centre of gravity, and then tuck the bike underneath them, to achieve greater ground clearance.

..It sounds to like the part in bold is where you're having problems. (I'm a poor hopper myself and that's the bit I struggled to even semi-master.)