Is there a way to reset the "water in Fuel" message. I got the message and changed the filter, but the message stays on. Also I poured the contents of the filter into a glass bottle and let it settle and there is no water from the filter. Any ideas are greatly appreciated.

unplug the sensor if the light remains on you could have a shorted sensor circuit

You may also have a bad Water in Fuel sensor. Seeing it is a 2007, I would take it back to the dealer and have them replace it.