Basically, when a standard is created the standard will likely use patented technology. Think about H.264. It isn't free. However, it is open (anyone is allowed to create hardware and software using the standard, so long as they pay the fee). Also, that fee is the same for everyone. These terms are FRAND (fair, reasonable, and non-discriminatory). It's essential for standards to ensure competition.
Then there are things that aren't standards. I'm not saying that you should agree with patents or anything like that, but they do exist and this distinction is made. If you hate patents (and I'm not saying you shouldn't), then they're all bad and we should get rid of them all. Disclaimer aside, let's say that you patented having 3 buttons on a phone (home, back, menu) ala some Android phones. There are many other ways to implement that functionality. Maybe that's the best combination of buttons and users love it. However, even in the Android world, we see phones with on-screen keys and no buttons, ones with 4 buttons, etc. You could even do something cool like a touch area with swipe left for back, touch for home, and swipe right for menu. Nothing there would kill your ability to create a device worthy of people spending money on. Taking a real-world example, let's look at Apple's bounce-back function for over-scrolling. Android 4 now does a highlight on over-scroll rather than the bounce-back. While a user might say, "the bounce-back looks better", it doesn't prevent a party from creating a device worthy of users' money.
Now, if you can't send signals using the technology that cell sites use, that does prevent one from making a device worthy of users' money. Those patents are standards essential. Now, when groups set standards, they will work around the patents of any company that doesn't want to license their patents under FRAND terms. However, companies want standards to use their technology because while they might not be able to extort money, they're guaranteed that everyone will use it. There's a big distinction between things you have to license and things you can implement differently with a little creativity and, as such, we treat them differently.
In the Apple/Motorola case here, Motorola (along with others like Nokia, Ericsson, Siemens, others) helped develop the wireless standards. They have to license their patents under FRAND terms. However, many of them want Apple to pay more per device than competitors. Part of this is that Apple has sucked up most of the profit in the industry and they want it back. Before Apple, Nokia was doing pretty well. Now? Motorola had been sliding for a bit, but Apple certainly helped that along by creating much better devices than pre-Android Motorolas.
Basically, there are patents that you're required to use and since you're required to use them (you can't build a phone without them), they have to be licensed under fair, reasonable, and non-discriminatory terms. The FTC looks like they will recommend that the government file suit against Google/Motorola over what the FTC sees as Motorola abusing these standards essential patents against Apple and Microsoft (http://www.bloomberg.com/news/2012-11-01/ftc-staff-said-to-f...).
So, this isn't a suit about Apple pushing UI patents against Motorola that got tossed here. This was Apple trying to get Motorola to license their technology under FRAND terms.
It seems that the disagreement is over the percentage model that Motorola wants. Motorola wants 2.25% of the full retail price of the device. So, if you make a dumbphone for $35, you pay 79cents. If you make a 16GB iPhone 5, you pay $14.63. Somewhat ridiculously, if you make a 64GB iPhone 5, you'd pay $19.13. Apple seems to be arguing that FRAND means that you can't discriminate like that. Motorola, still losing money, wants a large portion of those profits while still being able to profit off of cheaper devices. One can make the argument that the percentage model is non-discriminatory, but it doesn't fly well by me. Non-discriminatory isn't with respect to the price of the device or the money you're making off of it.