It is possible to detect a rootkit from the same system using a tool such as RootKitRevealer but it is not gauranteed. RootKitRevealer is a very effective program but the RootKit writers have already began to attack RootKitRevealer, which is why Mark keeps releasing newer versions to combat the problem. Just make sure you have the latest version. Otherwise you have to scan the drive from a Bootable CD or another system.
The problem is true RootKits can severly compromise core Windows System files which means cleaning it may make the system unusable.
Protection is the same as with other Malware. RootKits install through the same security holes that other Malware use, so being proactive about patching, using updated AV and a firewall will also protect against RootKits.
If you want a software solution, you need to get a program like
ProcessGuard. AntiVirus companies are working on their own solution.