Lip service. This is all lip service to increase interest in the sport. I don't believe Ferrari beat Mercedes on pace and neither do Hamilton or Rosberg. However, the company line right now is that Ferrari beat Mercedes fair and square.
The problems started in Q1. Mercedes used a set of medium tires in Q1. I believe they did that to preserve a set of hard tires for the race. They likely anticipated 3 stops all resulting in a set of hard tires being fitted. With hot temperatures and an abrasive track 3 stops were expected to be the normal strategy and I believe Mercedes used a set of medium tires in Q1 in anticipation of that. Eddie Jordan called them out on the podium for it as well.
The next strategy mistake by Mercedes was calling Hamilton and Rosberg in on that first safety car. Apparently they were still expecting high degradation and called their drivers in to the pit (per their pre-race strategy). Vettel had shown an ability to stay with Hamilton up to that point and stayed out on track. The end result of this decision was Hamilton lost 10 seconds to Vettel in traffic. That 10 second deficit ended up being the final deficit. It would have been one Hamilton may have been able to close with another fresh set of option tires, but unfortunately the team didn't have any. Evidence of the ability of a set of used options can be seen from Rosberg's pace from his final stop to the end. After Lewis complained the team put Nico back on track on a set of used option tires. Nico closed the gap to Lewis, but only a little bit before leveling out.
In the end Ferrari was on pace with Mercedes all weekend in S1 and S3. Each of those sectors has a very long straight. That suggests Ferrari is on par in terms of straight line speed. However, in S2 almost all weekend Mercedes had the edge (considerably in practice) where downforce is concerned. This bodes well for Ferrari at Monza (wouldn't that be something). However, that suggests Mercedes is equal to Ferrari in terms of speed while retaining a bit more downforce. The end result is going to have to be strategy wins by Ferrari (or losses by Mercedes) not straight up wins.