Fountain pens are supposed to be held lightly, so much so that someone should be able to pull it right out of your hand without friction (apparently schoolteachers once did this to test students' proper grip). Additionally, because of the water-based ink and capillary action of the pen, very little pressure is needed to mark the paper. Fountain pens are also able to be held at a greater angle than most other pens allowing a grip where the pen lightly rests on the back of the hand. This provides the ability to write for long periods without fatigue.
This is in contrast with ballpoints which require a significant amount of pressure to mark and which also cannot mark at the greater angle required which would allow the pen to rest comfortably on the back of the hand. This leads to all kinds of awkward hand positions that people learn to write with (a teacher or student will be able to attest to the numerous hideous and painful hand contortions some students employ) and more rapid hand fatigue because of the pressure required. It is not uncommon for carpal tunnel syndrome to develop in writers of ballpoints, and for doctors to subsequently recommend the switch to fountain pens. I also find that it is considerably more difficult to produce good handwriting using a ballpoint rather than a fountain pen. The hand positioning and technique really makes all the difference.