The question is not whether or not you and your cofounder disagree. The question is whether you can nonetheless find a way to make decisions and move on. If every disagreement causes your progress to stop dead, you've got a problem. If every disagreement is resolved in favor of the person with the loudest voice, you've got a problem. But it is in fact possible to make progress even with a team full of people who disagree, provided everyone is sufficiently open-minded, mutually respectful, and willing to indulge in whimsical experiments.
A lot of startup stories contain moments in which the cofounders had big disagreements; e.g. the time when Steve Wozniak had to be dragged kicking and screaming into quitting his day job with Hewlett-Packard.
What I've found, however, is that cofounders are especially tricky to integrate. I think once you have a running app/business it gets easier, but that entire process of taking something fuzzy and making it concrete is just a very difficult process for some folks. People are really good at BSing! Heck, if there was a prize for sitting around talking about startups it'd be a big bunch of folks winning it (myself included at times). But once you move past idle talk and start feeling for a market and a problem? It's not so sexy any more. And then when you're talking about all the hours that's required? People have a tendency to melt into the woodwork.
The ones that are extremely motivated are usually that way because they're emotionally attached to some concept -- and that concept may or may not be workable in the market. Which means it's like pulling teeth trying to have an honest conversation about viability.
Then there are the technology bigots, of course, and the "idea" guys.
I don't know about other startups, but the one I'm working on now is a pretty big commitment -- big enough that my "day off" is basically taking a long lunch today and surfing HN. The rest of the week, day and night, I'm working.
I don't see that combination of willingness to work on something that might not be hot at first and also being able to pivot when needed as being very prevalent. It's probably just me, though.
“Genius is 1% inspiration and 99% perspiration!” - Edison