While Cisco did buy the registered trademark "iPhone", it might not actually be their trademark to use. Trademark law doesn't allow one to simply apply for all sorts of trademarks and then allow the owner to enforce them in arbitrary ways. Trademark law is actually very restrictive in what one must to to get and maintain a trademark.
Descriptive Marks. The trademark iPhone falls under the trademark category of descriptive marks. That means that the mark describes the underlying product in the way that "All Bran" or "Holiday Inn" describe what their products are. Being a descriptive mark, it only becomes valid after it acquires a secondary meaning. Apple could easily argue that the "iPhone" trademark acquired that secondary meaning for their product well before it referred to Cisco's VoIP solution (which now looks like an underhanded attempt at extorting money).
Abandonment. Under US Trademark law, trademarks can be lost through abandonment. Generally speaking, non-use of a trademark for three consecutive years is regarded as compelling evidence of abandonment of a trademark. This is a protection in our trademark system so that someone can't go through and, say, register iDesk, iLamp, iEverything and just see if it would be useful to Apple someday in the future. Since the iPhone trademark that Cisco has was acquired in 2000 and they have done nothing with it for 6 years, there is quite an argument for abandonment of trademark.
Likelyhood of Confusion. This is where Cisco needs to prove its case should a court determine that "iPhone" is a legitimate trademark despite its lack of secondary meaning and abandonment for the better part of a decade. Here a court will look at, among other things, the strength of their trademark. Even here, Cisco faces an uphill battle. Their use of the iPhone trademark is amazingly weak. If you asked 1,000 people, how many would know that Cisco made an iPhone? Further, Apple can argue that by not enforcing its trademark against sites like Digg, Reddit, and countless blogs, Cisco did abandon the trademark by allowing it to be associated with a different product. Apple's lawyers will likely request any and all letters of trademark infringement that Cisco sent in response to the thousands upon thousands of postings linking the iPhone with Apple. A trademark holder is required to defend their trademark against being associated with competing products and companies. Cisco has completely neglected this duty and has probably hoped that the iPhone's association with Apple would help bring them some money - something a trademark holder is not allowed to do. If Cisco cannot prove that they have defended their trademark from being associated with another product, the trademark ceases to be valid. For any Digg readers who may come upon this, I'm sure you remember the
Digg Blog entry lamenting the fact they they had to enforce their trademark against others using the term "Digg" or loose the trademark.
Lucky for Apple, our trademark system has many protections built in to it to prevent trademark holders from making a quick buck. Cisco will have to prove that it has a valid trademark to begin with, that it didn't abandon it, and that it took steps to defend that trademark when countless postings online used it in conjunction with Apple. Even if Cisco is able to fight those battles and win, they still face one more challenge - the iSomething challenge. Apple can argue that the lowercase "i" followed by the capital letter of a product is a distinctive mark belonging to them and that iPhone plays off the popularity of iMac, iBook, iPod and that when something is labeled iSomething, consumers naturally associate it with Apple. Will Cisco be able to defend iPhone as a trademark? They haven't so far, but I guess time will tell.
EDIT: CNET's News.com
uses these arguments.