Although a notorious stigma of Flash games, there is in principle nothing stopping you from selling it via "traditional" means - portals, ecommerce, direct sales. Binding of Isaac being a well-known example. But of course, getting on sites like Steam with a Flash game might be ... *ahem* troublesome. Practically, Kongregate, Newgrounds and the likes with ad revenue are usually the first (and unfortunately often the only) choice.
VVVVVV and Isaac got on Steam, so it's not impossible. From outside of Steam, Defender's Quest sold well and it's main marketing strategy was Kongregate demo, so it is possible to sell your game, if it is of a higher quality.