Firstly, flyer collections in cafes are often not prominently displayed. They'll usually be sitting in some corner of the cafe. And they often get a bit mixed up with other stuff. Of course that's a risk on the boards, too. But it's not so bad.
Also, advertisers often leave quite big piles of twenty or thirty or more in cafes. While some do get taken by patrons, the remaining ones often get thrown out by cafe staff when they've been there a while. And if these areas aren't well maintained then other brochures can end up obscuring yours pretty quickly. In both scenarios if you've spent a lot of money on glossy flyers this is just money down the drain.
The noticeboards, on the other hand, aren't patrolled by shop staff so often. And while some can get a bit cluttered, your ads can usually be visible for the whole time they're up there. If you've pinned, say, five flyers to a big noticeboard they're much more likely to stay up until they're all gone. That can result in a very good ROI.
That said, cafes can be a good choice if you're seeking a young demographic from the inner city with high disposable income. Fashion shows, theatrical events, hairdressing salons, and similar ventures go well in such places. But if you have a business such as plumbing, or gardening, obviously, these locations aren't so great.
Noticeboards that target a certain demographic exist, too. There are many such boards on the university campuses in Perth for example. If you have a product that would appeal to this youthful demographic it could be an extremely effective way to advertise. Refurbished computers come immediately to mind.