They used to live in Northwest Washington State. Although a passport wasn't necessary for travel into Canada at that time, perhaps as a result of Stanly Dunham being ex-military, they just got one as a matter of course. (or habit.)
I’m still suspicious of the reasoning, and it seems to me that obtaining the passport has to do with an unwed pregnancy, and perhaps Dunham’s desire to travel to Kenya to have the baby and/or convince Obama to marry her by getting family approval. Of course, all this would have to fit in the timeline, and off-hand I’m not sure if it does.