What makes you think they aren't? That's the problem with a lot of software patents: people can just run into them (or be accused of running into them and subject to the resulting legal proceedings) without even knowing they were there. Then, suddenly, possibly after years of their own R&D, they get hit with paying royalties on something that had nothing to do with their own development work.

If there was no patent system, they would just use the end result without compensating Motorola for all the work of developing the technology.

Perhaps, but if they're really only trying to make carbon copies of what Motorola were doing, then Motorola have a huge first mover advantage anyway. Specifically, they have as long as it takes to commercialise their R&D work before they have to disclose it, because the work is a protected trade secret like any other up to that point. So as long as they keep innovating in significant ways that others couldn't, they will remain years ahead of their competitors in the market. That seems like a natural and compelling commercial incentive to me, without any need to add artificial benefits via patents.