I've seen this before.
1. Unplug the phone from the stereo and unlock the phone. Then plug it back in again. Repeat a few times...if that doesn't work....Push and hold the top button and home button of your phone for 10 - 15 seconds. Like taking a screen shot but longer. This will hard reset your iPhone.
2. If that doesn't work....Hard reset the stereo. Use the battery switch. Turn off the power for a few minutes. Then back on again.
3. If that doesn't work... Replace the white iPhone cable with one from Apple.
4. Also check to make sure your phone has the latest software from Apple. They have patched IOS 7 and there is an update.
5. Finally, trickle charge your boat batteries over night. Sometimes if they are low, you'll find the stereo starts to get flakey.
Generally speaking I have found #5 to be the issue.
Edit: in many cases, you can ignore the message and a few minutes later, the phone will start to charge... But if your iPhone cable is after market, then see the link in #3.