Marquez's 10-race winning streak ended in Sunday's Czech Grand Prix, where the Honda rider could only finish fourth behind Dani Pedrosa, Jorge Lorenzo and Rossi.
In his Honda years, Rossi won 31 out of 48 races as he notched up his first three top-class championships in 2001-03.
The seven-time MotoGP champion thinks Marquez's achievements receive more media praise than his ever did.
"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," said Rossi.
"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."
Rossi suggested that the quality and attitude of Marquez's current opposition is a factor.
"Maybe it's the rivals, because we are better rivals than what I had," he said.
"We never complain about our bikes, more or less.
"Whereas in the past especially [Max] Biaggi complained that I beat him because I had the best bike. It was funny...
"But in the end I changed bike and I also won with Yamaha, and then [it was said that] I won because I didn't have rivals... It was never ending.
"You cannot say anything [bad] to Marc because he won 10 races. For sure at this moment he is the fastest rider."
Rossi reckons it only took a tiny deficit to halt Marquez's winning streak at Brno.
"I like Marc, but it's great to finally beat him after 10 races," he said.
"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.
"Marc will not change his mindset. He knew in his mind it could happen. We know that we can beat him.
"Maybe this time Marc lost time or made some mistake with the set-up during the weekend.
"MotoGP is like this: if you are not able to be at 100 per cent and maybe you have some small problem with the setting, you finish behind."
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