I've read in more than one place that its more fun to ride a slow bike fast than a fast bike slow....
So true...the great thing about the ninja is it's one of the few (only?) 250s that will do freeway speed (in the northeast anyway) all day long no problem, and STILL have a little room for more just in case.
If you've got the cash the 500 would be a great choice too, if only because the suspension is WAY better than the 250 (however you can always slap some 500 shocks on a 250 for like $50 if you do it yourself).
Like someone else already said...it's all about self control. I've ridden a Suzuki Intruder 800 since I got my license and have not had any problems whatsoever. IMO a hooligan will be a hooligan whether on a 250 or a 1000.
For a first bike I don't think displacement is important at all (barring insurance). What you should be considering is will the bike be a good bike for LEARNING to ride on, ie. is it going to let you develop as a rider? Is the torque curve basically flat or is it the bike going to lumber up through glitchy caburetion to 7k rpm, and then suddenly you'll be gripping the bars for dear life? How's the clutch? Does it engage nice smoothly with a big friction zone, or is it practically an on/off deal...and do you think that a sensitive clutch is going to make it a pain to ride or help you to learn better clutch control? Lots of other things to consider (brakes, riding position, drivetrain, vibrations, etc. etc.) but don't want to make this TOO long.
Unfortunately most of this stuff can only be figured out by riding the bike, which most dealers won't let you do, and the MSF only gives you a couple choices and they usually won't let you change bikes during the course. What I'd recommend is that you ask yourself what you want your bike to do (twisties, boulevard cruising, cross-country road trips, all of the above), then shop around, read reviews, find a friend or a friend of a friend or anyone that has a bike you're interested in and see if they'll let you try it out. Rather than just asking "hey guys what's a good beginner bike?" try "what would you guys recommend for a beginner looking for ."
Once you're fairly sure what you want your bike to do, it'll be easier for everyone else to help you out.
Ride safe!