The reigning world champion sits 77 points clear at the top of the standings, though his stunning 10-race winning streak was ended in Brno at the weekend.
Marquez could only finish fourth with Dani Pedrosa winning while Rossi and Jorge Lorenzo completed the podium places.
With the 21-year-old firmly on course for a second MotoGP title, seven-time world champion Rossi believes there is a difference in attitude towards the pair from certain quarters.
"The biggest difference between my period and Marc's period is that when I won in 2001-03 with the Honda, not everybody but a lot of people - especially the journalists - said that I won because I had the best bike," he is quoted by AUTOSPORT.
"Now with Marc, racing with Honda, he's won a lot of races but it's said that he made the difference.
"I don't know why there's this difference between me and him, for me it's difficult to understand."
After Marquez missed the chance to become the first man to win 11-consecutive premier-class races at the start of a campaign, the gap between him and Rossi now stands at 90 points.
Despite the sizable difference, Rossi was pleased to reel the Repsol Honda man in somewhat ahead of the remaining seven races.
"I like Marc but it's great to finally beat him after 10 races," the Italian added.
"It looked like Marc was not at 100 per cent with the setting of the bike - finally!
"This happens to everybody a lot of times but Marc was always able to be very, very strong in the race. This time he wasn't able to ride at the maximum."