While Vettel's dominance proved a turn-off for many fans, and prompted teams to adopt the heavily-criticised double points rule for 2014, Whitmarsh thinks F1 should not be so hard on itself.
Rather than treat a one-sided campaign like 2013 as cause for alarm, Whitmarsh thinks F1 should instead big up the excitement it has delivered more often than not over recent years.
"We jump on a bandwagon very quickly, particularly with Vettel's nine straight wins," Whitmarsh told AUTOSPORT.
"Over the last few years we have had some great championships. Last year was not the most classic championship, but there were some quite good races in fairness.
"People have short memories and also there is this cynicism that appears - and I hate it.
"This is a great sport. People always talk about a golden era - but I think the last few years have actually been fantastic in terms of the racing and the overtaking that was created with KERS and DRS."
Vettel will be chasing a 10th consecutive victory when the 2014 season starts in Australia in March, having not been beaten since last year's Hungarian Grand Prix.
That run of form has left some suggesting F1 is in need of a new winner in 2014, or else it risks viewers giving up on the season early on.
Whitmarsh admitted that no sport benefits from having the same man triumphing all the time, but thinks F1's success is not dependent on Vettel being knocked off the top.
"Any sport needs different winners," he said. "It needs unpredictability.
"You want a sport where, on Saturday night, people are wondering who is going to win the next day. And then you need that until three laps to go you are wondering who is going to win the race.
"On a personal level of course I want a different winner, but I don't want to get on that bandwagon [that we need it].
"We are so good at talking our show down that it frustrates me because we have done a lot. We have had some great racing and great championships recently."