No matter how you're going, the soundtrack is the most important part.
Of course, the key question is whether that soundtrack will last for 3 hours or for 30, and whether you'll have to endure silence for takeoff and landing.
For the cross-country traveler(/ing student), whether to fly or to drive is a huge issue. So, as you need for any good decision-making, here's a little comparison for you.
Ah, the all-important question. Here's the deal: you can usually get pretty cheap flights if you plan right. Flying on days that aren't weekends or Fridays will definitely save you some money. If this means coming home a day earlier from break or missing your one 12:30-1:20 class on Fridays (depending on what it is! I'm not advocating class skipping), it's probably worth the money. By doing that, you'll shave about a hundred dollars off your airfare. The same goes for flying out of smaller airports to avoid airport fees (ie, Midway rather than O'Hare in Chicago) and packing light (baggage fees are crazy, and you can fit all your clothes in a carry-on sized suitcase. *Note: Southwest flies bags free! My personal favorite airline!) It's easy to see what your airfare cost is; for driving, remember to calculate food and hotel rooms as well as gas. On the whole, the cost will come out about even for 3 days of driving. There's no way for me to say for sure which will be cheaper for you because I don't know where you live, but there's are the things you should keep track of when looking into cost.
Airports=more fun alone; driving=more fun with friends/family. Roadtripping with people you like/want to get to know is always fun. If you have friends who live in interesting (or even uninteresting!) places on the way home, offer to drive them! This will save you money and sanity on those long boring roads. On the flipside, airports can be fun if you like exploring little coffeeshops and people watching! If you have no layovers and have no specific airplane love though (it exists; you'll know if you have it), your trip will simply be lots of reading/sleeping/jamming to your ipod.
What you Own
What are you planning to bring home? This will make a difference (especially if you're a musician!). For the summers, you'll probably want to bring more. Weigh the issue of driving and having room in your trunk for those suitcases against the cost of luggage fees (and the hassle of getting your bags under 50 pounds apiece). For shorter breaks (Thanksgiving, spring break, maybe even Christmas), you can probably swing a carry-on bag.
Of course, all of this depends upon whether you have a car to bring to school, whether you will need to have a car on campus (look up your public transportation; if you're going from city to rural or vice versa it will change), and whether it's conceivable for your parents to drive you out to school and then drive back alone.
Go forth and seek yourself a long and winding road/airway!