This is actually somewhat common and dare I say 'normal'. There are multiple systems at work when using navigation: GPS, Wireless data, CPU and GPU of the phone to render the display, provide voice navigation, etc. Plus the persistent display. This is a demanding task of the device and will cause it to get warm. Mine does this, my Galaxy S2 did this. Once are done using it though the phone should return to normal operating temp. If it doesn't then you might have an issue.
It's difficult for a mobile device to maintain a constant signal due to changing towers while in motion so add that to the list of what's operating for navigation and there you go. When a tower was down in my area my S3 struggled to get a signal and it would get hot just trying to Google something. It's normal, as RC said, it does have protection against overheating so if that doesn't kick in you have nothing to worry about.
Anything that used large amounts of power will cause the phone to heat up. The battery will heat up when a lot of power is being pulled to run things. GPS navigation is probably the single most intensive thing you can use a phone for. The phone must maintain a constant data connection to the towers to get map updates/navigation directions/audio feeds for voice directions/traffic updates/etc. This will heat up both the battery and the antenna itself. In addition it must also maintain a GPS lock with the satellites, which needs to keep at least 4 in sight at all times to be accurate, more often you are looking at 10+. Add to this anything the phone may be doing in the background like regular email syncing, facebook, etc. and it can heat up pretty quick.
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