It was put in place because Qualcomm owned the most important piece of the package and leveraged their strength to get a percentage of the whole phone's value.

It was put in place because Qualcomm owned the most important piece of the package and leveraged their strength to get a percentage of the whole phone's value. Everyone got locked into the uniform Qualcomm licensing agreement and despite the change in the cost structure of modern phones, no one has had the leverage needed to force Qualcomm to change their licensing.