The Rebel is boring. You'll outgrow it in a couple weeks. My wife wanted one until she rode it a the MSF RiderCourse. It's woefully underpowered for freeway riding. If you wring every ounce of power out of it, you can get it up to 75 MPH.
The Ninja is a small bike; it's very light and nimble. It's not going to set the world on fire, but it'll be entertaining for at least a year until you're ready to move up to a larger bike. You'll have no problem getting it up to speed on the highways. It holds its value well; when you decide to move up to a larger bike, you'll get most of your money back on the Ninja, especially if you buy used.
My wife ended up getting a Ninja 500R. It's not too much bike for starting out... anything with less than 4 cylinders will make a fine starter bike, assuming it's not too heavy. Even a 650 twin is OK. Once you move up to an inline four, you're into racing bikes... that would be a bad idea.
Try the two bikes out. There are people on craigslist.org that'll let you take them for a quick spin in a parking lot. I know this goes against everything I just said... but buy the bike you like better. That's really the best advice anyone can give you.
EDIT: Looks like Yahoo! Answers was sponsored by Honda today.
