I think the Dragons at Winterhold only start appearing after you've become the Archmage. At least it seemed that way to me, but I suppose it could also be main quest related.
I get tons of dragons and I haven't done any main questlines except visiting greymanes, companions (Harbringer), and college (Archmage). Like darklord, I really don't mind. A dragon doesn't live long at the college Anytime I need a soul I just Quick Trip to the college 3 or 4 times!