I don't believe a timeline thumbnails feature is in Flowplayer 3.x.
Keep in mind that Flowplayer is based on the plugin concept. Rather than create one huge SWF with the bulk of features most people won't use, the player relies on optional plugins to extend its functionality. The plugin architecture is documented, and this type of feature could be accomplished by creating a custom control bar.
Note that clickable timeline thumbnails will need a streaming server, or at least pseudo-streaming. Otherwise, you won't be able to seek to a point in the timeline until it has been downloaded. For short videos not a problem, but then, they don't need thumbnails.
For the latter, and if you have FFmpeg take the snapshots, you will first need to make sure the file has been passed through a metadata injector that identifies keyframes and positions. You'd need to pass the keyframe positions (or a subset of them) to FFmpeg, so that your thumbnails are only on keyframes.