While they share some features, I think they both have different target audience.
webpack wants to help application developer, by supporting many different module types, weird configurations, silly dynamic dependencies, stylesheets, images, etc.. The output doesn’t need to look pretty as long as it works.
rollup wants to help the library developer, by supporting a pretty output format, tree shaking. It focus on ES6 trying a bring in new optimization possiblility, that were not possible with legacy module systems.
It depends on your needs.