A couple reasons I can think of.
Any time you can avoid putting a pilot in harms way, take it.
Additionally, some of the Tomahawk strikes are utilizing time on target planning techniques that allow for multiple simultaneous strikes within a few seconds of each other. To get the same effect with airplanes, you'd need many more planes flying, and the more planes you have overhead at any time, the better chance the Iraqis have of shooting someone down.
JDAMs are incredible, but remember, when your only tool is a hammer, all your problems look like nails. There are times when it's worth the cost of using Tomahawks.