Apple wants to push their Lightning port, like the article in the link says. They will not force bluetooth headphones, that would be useless.
Of course they get the sales, but Apple sells more than just iPhones. And if they can make their Lightning port a new accepted standard maybe more companies want to use it, or more companies want to make Lightning port headphones. Which all means more dollars for Apple.

Basically, doesn't change anything though. People almost never use any other headphones, with their iphones, to begin with. And paying royalties to Apple, from third parties. Would make the cost of 3rd party headphones, basically be equal to the apple ones. Making their exsistance moot. Apple could just stop selling headphones and make other companies supply them. Since they still have to pay the lciensing fee.

Well i agree they will not make the Lightning port their standard for headphones to get tons of money (from the port itself or royalties). I think for Apple the bigger reason is brand association. You buy Apple you get the 'wonderful' Lightning port, way better and newer than the old jackplug. And sure when the new iPhone comes a lot of people (special non apple fans) will be turned off, telling that Apple forces it onto you. But Apple will not care, because all the lovers will buy it anyway. First it's the iPhone and later all other Apple products using the same Apple standard. It's what Apple always has been doing, you love our product so you use what we tell you. 

For Apple the choice is pure business. If a Lightning port can persuade people (and for sure there are more than enough) to buy an iPhone or other Apple product, than it will turn into a lot of dollars for them.