Hail punches through solid coverings because they are rigid. They nearly instantaneously stop the hail which means they absorb all of the kinetic energy of the hail very quickly. They don't have a good way to dissipate that energy as rapidly and it goes into breaking the structure of the covering.

Nets are flexible. The energy of the collision goes into accelerating the net at the point of the collision. The net can quickly spread that energy into accelerating the surrounding areas of the net and so on. Unlike with a rigid cover this is not nearly instantaneous, so you don't have all the kinetic energy of the hail being poured into the net at once. That and the ability of the net to rapidly spread energy means that you don't get enough energy anywhere to break the net. It just stretches as it decelerates the hail.

You can see how this works by watching a soccer game and observing how the nets at the goals stop balls. Hailstones that weigh more than a soccer ball are extremely rare, as are hailstones that are falling faster than many strikes and penalty kicks in a professional soccer game, and you don't see many soccer balls breaking through the net.

People have calculated how fast a soccer ball would have to go to get through the net and found that it is over 220 mph. The largest recorded hailstone is estimated to have had a terminal velocity of 168 mph, based on size, mass, and atmospheric conditions. That hailstone had about 16% more kinetic energy than a 220 mph soccer ball and so might have broke the net, but soccer nets are by no means the strongest nets that can made. And remember that was the largest hailstone ever recorded--we are talking a once in decades event.