I noticed that both do the same thing, ex: caching, minifying.
W3TC is a framework. The intent is to optimize the origin (the stack the WordPress application runs on) and THEN what runs "on top" of it. A great discussion around that is available here: http://websynthesis.com/wsa/wp-content/uploads/2013/09/The-Truth-About-WordPress-Performance.pdf?utm_content=buffere8e5b&utm_source=buffer&utm_medium=twitter&utm_campaign=Buffer
So yes, Cloudflare and other similar providers like Yotta and the like may apply browser caching policies, provide multiple edge locations and even minify CSS / JS or optimize images etc, but it's important to know that as a framework, W3TC is integrated in with WordPress internals and also gives you control from inside WP Admin with regard to policies you can set around when content is purged, what is minified and what browser caching policies you have so that what any providers do is not just best practices as they define them or what a report indicates as "best" lowest common denominators that would "work" for anyone.
Here's what's common between CloudFlare and W3 Total Cache:
So, CloudFlare does everything that matters when it comes to serving content efficiently to the public at large.
On the other hand, I believe that W3 Total Cache's Object Cache comes in handy, as it could provide an increase in performance of uncacheable pages/content, like for example, wp-admin, which'd be crucial for logged-in users.