Certainly flatness is a big incentive. Our reaction, however, is against the comment "There is only one, and one reason: their country is flat."
That's simply not true. As the article points out, the Netherlands, like other countries, had a large decrease in the use of bicycles in favor of the car. It wasn't until political protests of the 70s and 80s that that trend reversed itself.
But having hills is not a complete disincentive. I used to live in Gothenburg, Sweden, which has a very extensive cycling network, with many people bike commuting, etc. It also has hills. The key thing is that it's not all hills; the bike paths tend to follow the flat. But I lived near the top of a hill, at about 200 feet above the central part of town, and plenty of people would do that commute every day. (Not that I particularly liked it.)
It's of course a very complicated set of interactions. The city also has good public transportation, so if the weather is nasty it's still easy to leave the bike at home and take the trams and buses to work.
Or consider Trondheim, Norway. According to one web site, "18% of the population of Trondheim is using their bike as a daily means if[sic] transport to work or school." Trondheim is not a flat city, and certainly Norway is not a "mostly flat country."