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.