It is pretty hard NOT to get 1,000,000 if you manage to play through Gold Sparkster mode. If you don't want to attempt that, just play on Hard (see the Devotindos Defiler guide to learn how), and it's really not tough at all. In fact, I got the 1,000,000 and 60-minute-clear achievement on the same run... so if you take your time and get all the items/enemies you should get 1.2m+.
On the flying stages make sure you extend your combos as long as possible (watch the combo meter in the upper-right corner) by using your charge-X move to blow up mines. It's very lucrative, especially on 4.1 (you can get 130,000+ just in the first section!).
You won't hit 1,000,000 in Normal difficulty, so don't bother trying.