Nah, the Iron Islands are their own political entity. It's Ned's job to keep them in line because they have a habit of rebelling, and Winterfell happens to be closest to them. If they were down south, then it would be up to the Lannisters, or Dorne to handle them.

Also, The North didn't rebel on it's own.

If I recall, it went something like this.

Regar Targeryan "Steals" Lyanna Stark (Betrothed to Robert Baratheon), Mad King Ares kills Ned's father and brother.
So, Ares has now angered the Starks and the Baratheons, so there go the North and the Stormlands. Meanwhile, the Starks are bound to the Tullys by marriage, so the Riverlands also rebel. Jon Arryn raised Ned and Rob (And may be tied to the Tullys by marriage as well, I'm not sure when he was married to Lyssa), so the Vale gets in on the conflict.
Technically, Ned has more cause (a stolen sister, dead brother, dead father), but he's unambitious, so Robert (stolen fiancee) takes the lead.
This leaves the Westerlands (Lannister), Dorne (Martell), the Iron Islands (Greyjoy), and the Reach (Tyrell) as loyalists. I'm assuming the Ironmen didn't actually contribute very much, even if they didn't actually join the rebellion.