The Team Sky rider rode through a chorus of jeers and whistles in the western city of Mouilleron-Saint-Germain on his way to the start line, three days after being similarly booed at the teams' presentation ceremony.
Froome was cleared last week of any wrongdoing by the World Anti-Doping Agency (WADA) and the International Cycling Union (UCI) after testing positive for excessive levels of the asthma drug Salbutamol during last year’s Tour of Spain.
Sky spent over a million euros to defend Froome in the case, leading some to question the fairness of the process.
Team Sky principal Dave Brailsford said he believed the process will eventually be fair for everyone, after the British team said it had shown the likelihood of 'false positive' results.
"For me I'd be looking at that…. 'Thanks very much for the investment, we can use this to keep on developing, to make sure the rules are better, redefine them to protect innocent riders," the Welshman told reporters on Sunday.
"I would not take it from another angle which is one rule for one and one rule for another."
"At the end of the day we have a set of rules and we expect them to be reviewed and updated and kept on point."
Public opinion in France, however, remains hostile towards four-times winner Froome, who is hoping to join French legends Jacques Anquetil and Bernard Hinault with five victories in the race.
One banner held up by the side of the road on Saturday read "Froome out", while another read "Froome go home".
“We have to just deal with it, that’s all. It’s not the first time, that’s the way it is,” said sports director Nicolas Portal.
Froome also had problems on the bike as he crashed five kilometres from the finish in Saturday’s opening stage, losing 51 seconds to two big rivals, France’s Romain Bardet and Dutchman Tom Dumoulin.
"I know there’s always a high risk of crashing in the first week," said Froome, who had bandages on his elbow and knee. "It’s never nice to lose time, never good to start on the back foot, but there’s a lot of racing to come."