Facebook allows ads to appear inside Instant Articles. Publishers can keep 100% of the revenue if they sell the ads, and Facebook gets its standard 30% cut if it sells the ads.
With the launch of Instant Articles, Facebook provided guidelines regarding the ad formats supported by Instant Articles. One of the constraints was that no ads can appear above the fold (so that when somebody first opens an Instant Article, they will not see an ad). This would help with rapid initial loading of pages.
In late March 2016, Facebook announced an expansion in the permissible ad formats. In particular, support for native ads as well as video ads was announced.