Professional 2D animators use Toon Boom, probably. I think some webtoon animators still use Flash. I heard My Little Pony is animated using Flash. Professional Japanese animators still animate with paper and pencil, though I'm not sure what software they use for coloring. I'm not familiar with what the 3D industry uses, but I think 3Ds Max and Maya are two of the more popular ones. Blender is well-known too but I'm not sure if it's mostly used by amateur animators or if it's also widely used by professionals.
Most stickfigure animators are amateurs. I really wouldn't consider people joining contests and winning cash prizes as "professional animators." Most of the stickfigure animations you've seen (that weren't using Pivot) were made using Adobe Flash. Most of the good RHG animations were made using Flash. EZToon is also popular among stickfigure animators. I've also heard of some people starting animation with MS Paint and Windows Movie Maker, if you could believe it.
