The iPhone uses assisted GPS to improve the accuracy of the location system using GPS and cell towers. Wi-Fi networks are used to help determine the device's location; this is called a hybrid positioning system (XPS).
In particular, iOS taps into (and helps to update) the Skyhook Wireless database of Wi-Fi hotspots and their locations. You can even submit new access point locations through their website to help improve the database (but your device will automatically upload information to keep this database fresh).
Here's information from Skyhook Wireless and an article from Apple with more detailed information on iOS 5 location services. Apple's article also mentions that Wi-Fi + GPS are used to crowd-source traffic information.
If Location Services is on, your device will periodically send the geo-tagged locations of nearby Wi-Fi hotspots and cell towers in an anonymous and encrypted form to Apple, to augment the crowd-sourced database of Wi-Fi hotspot and cell tower locations. In addition, if you are traveling (for example, in a car) and Location Services is on, a GPS-enabled iOS device will also periodically send GPS locations and travel speed information in an anonymous and encrypted form to Apple, to be used for building up a crowd-sourced road traffic database. The crowd-sourced location data gathered by Apple does not personally identify you.
For your security concerns, read this Apple press release.