The reason for this settlement between Apple and HTC has very little to do with HTC's implementation of Android, which quite frankly, if that was the main reason for their dispute, Apple wouldn't have settled.
No, this settlement is about APPLE realizing it was facing a LOSING patent infringement battle against HTC and its LTE patents that could have lead to a sales injunction against all iPhone 5, iPad Mini and iPad 4 LTE models in the US.
The judge in the case had already cautioned Apple that he would have to be "overwhelmed with evidence" to grant their request to invalidate HTC's LTE patents. If he didn't invalidate those patents, it would basically be an air-tight case for HTC as Apple hadn't argued that they didn't use the technology covered by those patents (which is beyond dispute), only that HTC shouldn't have been awarded them.
It's not a surprise that the terms of the settlement were kept "confidential", but if they are ever released it will be revealed that it is APPLE paying HTC for licensing fees, not the other way around.
Unfortunately for Apple, they are involved in a similar case with Samsung in the EU with regards to infringements against Samsung's LTE patents in the iPhone 5, iPad Mini and iPad 4.
It's unlikely Samsung would agree to a settlement. Rather, it's more likely they'll play hardball and force a permanent sales injunction on those Apple products in the EU, which would land a crippling blow to Apple, ceasing revenue from their top three highest grossing products in their second most important market, and sending their AAPL share price into a spinning nose dive from which they may never recover.