Froome effectively wrapped up the yellow jersey in Marseille on Saturday by finishing third in the 22.5 kilometre time trial, increasing his overall lead ahead of Sunday's traditional procession into Paris.
An article in the Observer on Sunday suggested Team Sky's image prevents Froome's achievements being widely acclaimed, following negative publicity in recent times.
It began with Team Sky boss Sir Dave Brailsford's handling of questions regarding a package which was delivered to Bradley Wiggins during the Criterium du Dauphine in 2011.
The fall-out from that issue, together with hackers leaking information that Wiggins had received therapeutic use exemptions (TUEs) for the otherwise banned drug triamcinolone in the build-up to the 2011 Tour, his 2012 Tour win and the 2013 Giro d'Italia, has cast doubt over Team Sky's clean image and also raised doubts about Froome's performances.
Wiggins strenuously denies any wrongdoing and prior to the Tour starting, Froome signed a new contract with Team Sky and stated: "I've been here since the beginning and I've never seen anything untoward. I don't have any trust issues. I can't make it any more plain."
Cookson, the president of cycling's world governing body the UCI, told BBC Radio 5 Live's Sportsweek programme: "Firstly, it's an absolutely superb performance, there's no doubt about that. Historically not many people have achieved anything like this, so hats off to him.
"He has certainly shown that he is the strongest rider in the race, but he's not had it all his own way. He has fought and shown weakness now and then and we have had a very close race and a very exciting race.
"I think it is regrettable that people have a negative view of success. From my point of view as president of the UCI, I have to assure everyone that all teams are treated equally and that our anti-doping procedures, for example, are rigorous and independent with no conflicts of interest and so on.
"We have taken huge steps in our sport in the last few years to ensure that we are absolutely the best in the class, as it were, with anti-doping.
"There will always be resentment of success from some quarters, I guess, but Team Sky and all of the other teams are treated equitably and fairly and if there was any reason to doubt anyone's integrity then those processes would come into play."
