Magneto is a pragmatist, while Xavier is an idealist. To an extent, Magneto is right. If mutants are revealed and humans know about them, they'll want to capture them, dissect them, come to fear them, and so on. On the other hand, Xavier is right too, because without Magneto antagonizing the humans, the humans would be much friendlier to mutants - hell, they might not even know about the mutants, who could be happily hiding.
I think ultimately, I come down on Xavier's side. Not for any of the idealistic reasons he spouts, because I think mostly he is full of nonsense and simply hoping for the best. Magneto is willing to make the tough decisions to ensure the future is what he thinks it should be. But motivations aside, if you look at their plans there is simply one key difference. Magneto wants mutants to take charge now, violently overcoming human opposition. While Xavier wants humans to lay low and side with the humans, and eventually the mutants will be too large in number or too invaluable for their place in society to be challenged. Since mutants are apparently the next step on the evolutionary ladder, that basically means that Xavier sees fate as being on his side. They just need to bide their time, and if they hold out long enough, they'll win, once a critical mass of mutants in society is attained, and every human either knows or has a relative who is a mutant. That seems more feasible and pleasant to me than a bitter war where mutants take over everything and keep humans down with an iron fist.
But ultimately, I think either of their approaches would work. It's just that the two sides spend so much time fighting each other than neither course of action is actually chosen, and all the mutants lose instead. Although this is my view of things based solely on X-men First Class and Days of Future Past, and the bit of X-men lore I have picked up from here and there. If I'm off on something, don't pillory me for it.