UPDATED/CLARIFICATION: Responding to your comment "Currently all sites are on different IP's and servers due to their size."
Your server IP addresses (A Records) will stay unique/same. The IP is masked by Cloudflare's Anycast using different IP addresses across the world, depending where used can be identical or in similar range. They cache static content with a short expiry time; for non-cached content their servers proxy through requests to the actual server then forward to a user.
See http://www.quora.com/CloudFlare/How-does-CloudFlare-work for a detailed response from CloudFlare's CEO to a similar question.
Now Google "should" first of all understand how Cloudflare works as a CDN just like it does with other similar CDNs and security platforms.
Does Google care about same IPs no, unless there are spammy neighbors using it:
“… there was recently a discussion on a NANOG (North American Network Operators Group) email list about virtual hosting vs. dedicated IP addresses. They were commenting on the misconception that having multiple sites hosted on the same IP address will in some way affect the PageRanks of those sites. There is no PageRank difference whatsoever between these two cases (virtual hosting vs. a dedicated IP).” Cutts Blog
Should Google figure this out and be able to differentiate the Cloudflare masking yes. But has Google been found with incorrectly diagnosing spam yes, with probably less complex issues to Cloudflare. The question may be do you want to take the risk, or partial risk as you can actually use your own DNS and cloudflare (paid version) again hoping assuming Google will understand.
Hope this helps, curious as to how Cloudflare will respond to this, so please update. But as an SEO'r it would depend how much risk you want to take in this case.