I think these days , most people go indepentant because of the flexibility it affords, not "to save a few quid" - because it doesn't! A few years ago it was possible, if you got a really cheap flight, to do it cheaper than a package but not anymore.
Personnally, I will still go independantly when I can afford to, for the flexibility as I said, and to put money in the locals pockets rather than the tour operators'. If you use a bonded flight operator, or a credit card, there should be no problem.