The main pack, headed by then yellow jersey holder Cancellara, decided not to sprint to the finish line after rain and an oil spill combined to make the roads very slippery on the 201-km second stage from Brussels.
Norway's Thor Hushovd was angry because it dented his chances of claiming the green jersey for the best sprinter.
"What happened is not normal. Why would it be for Fabian to decide? I was not okay with this," Hushovd said.
Cancellara and company decided to play it safe after a massive crash had split the pack into three groups, with the Swiss in the front, Lance Armstrong and Alberto Contador one minute back and the Schleck brothers, Andy and Frank, a further three minutes behind.
Despite Hushovd's anger, Saxo Bank's Cancellara was praised by other riders for allowing those who had been caught in the pile-up a chance to catch up and regroup the peloton.
"Fabian is the big man of cycling physically, he is also the big man of cycling tactically," HTC-Columbia team manager Bob Stapleton told Reuters before Tuesday's third stage.
The Swiss, who won the Tour of Flanders and the Paris-Roubaix classics this season, also asked race technical director Jean-Francois Pescheux to discard the final sprint.
As a result, the peloton crossed the line at a leisurely pace almost four minutes behind stage winner Sylvain Chavanel of France.
Cancellara lost his yellow jersey in the process but the move allowed the Schlecks to stay in contention.
"Saxo Bank proved yesterday they are the cleverest team of the peloton," said Stapleton.
"Fabian did a masterful job. He accomplished multiple goals."