Cena surpassing Flair's title reigns... lots of problems with this actually and very few of them have to do with Cena being worthy, deserving, et. al.
Cena's title reigns and Flair's title reigns are different... vastly in fact. Even going back to his UPW days, Cena has always been in the WWE system. All of his matches have been within some level of the WWE confine, whether it be in developmental or on the mainline shows and programming. His current number of title reigns speaks to the level of confidence that WWE has in Cena as an entertainer, a money draw, or whatever other mark of success one wishes to apply. Still, those accolades only apply to the WWE brand when it comes to sports entertainment / pro-wrestling.
Compare to Ric Flair, a guy who essentially went everywhere and fought everybody during his active career whether he was the world champion or not. His title reigns are the product of multiple loosely connected at best organizations that had enough confidence in him to put the belt on him. WWF/E was only one stop during his illustrious career as the Nature Boy, a gimmick that persisted throughout his entire active career and still persists to this day. While WWE has officially recognized 16 of Flair's world title reigns, it has been noted by historians and Flair himself that the real number likely lays in the 20's somewhere.
So what it all comes down to is, does marketing Cena as the guy who beat Flair's title record equate to a profitable endeavor for WWE? Honestly, I'm not sure. We know Flair won't say anything against it's legitimacy, but others will. Does that matter? Hard to say without actually pulling the trigger. It probably won't matter to today's fan since Ric Flair is essentially a guy they've seen in video packages, perhaps on the WWE network, and who they know is a legend because WWE tells them he is. In other words, he's "point of reference" only for those folks.
So the question is, do I think Cena deserves to beat Flair's world title record? Well, based on my perspective and what I stated prior, my answer would be it simply doesn't matter. Why? Because Cena holding 17 WWE world titles is simply not the same as Flair holding a world title 16 times. It's apples and oranges.