Cloudflare and services like that such as Sucuri and Incapsula all provide DDoS protection services and (for their paid plans) a WAF.
If you make use of their free plan, then you are usually not protected from regular website attacks. Now the question - can you use it along with WebARX?
The answer to that is - it depends. Cloudflare for example has a "under attack mode" setting that will block our servers from accessing your site, thus possibly causing us to show that your site is/was down.
If your settings are all set to the default protection settings, then you should be fine and you can use all of our features.
If you want to see the full WebARX comparison table look here.