Maresca has made 85 changes to his starting lineups across all competitions this season - more than any other Premier League club - as Chelsea fight on several fronts.
Rooney argued that the constant "chopping and changing" of the lineup would prevent players building relationships on the pitch, urging captain Reece James and senior players to challenge Maresca's approach.
"Football is a bit different compared to years ago in terms of physicality and intensity," Maresca told reporters ahead of Saturday's match at home to bottom side Wolverhampton Wanderers.
"For me personally, it's impossible to play with the same players for 65 games a season - Champions League, Premier League."
'You need to rotate'
"I played for 20 years – it was not as physical and now it's changed. You need to rotate. This is my personal view," the much-travelled Italian manager added.
"I think you need to do that if you want to see a season like a marathon. Then, when you are in February and March, when it's the last sprint, you probably have to think in a different way. But at the moment, you have to think like a long race."
Maresca defended the quality of players he brings in and said he respected Rooney's opinion but suggested criticism of his rotation policy only emerged after they failed to beat Qarabag in the Champions League this week.
"I think that when the rotation is Andrey Santos - Brazil international player, Jorrel Hato - Holland international player, Estevao - Brazil international player, it's not about rotation," Maresca said.
"They are good, talented, young and, for sure, when they are young, you have to give them the chance to make some mistakes to be better.
"The same thing happened in the past with Josh Acheampong. But I understand that when you don't win games, the problem is rotation and all different things."
Hato was caught out for Qarabag's first goal and handled to concede a penalty for their second in the 2-2 draw.
Estevao ready to start
Estevao has primarily made cameos this season and Maresca said the 18-year-old is ready to start even though the Brazilian is still adapting to English conditions.
"We are trying to do the best for Estevao, helping him adapt to England," Maresca said.
"Last week he was complaining about it being too cold. Last week was still October, so imagine December and January - he has to adapt.
"He is happy, doing fantastic and for sure he's a talented player for this club."