Liverpool fans greeted City's players with boos and chants of "Going down, going down!" amid speculation over potential sanctions after the Manchester club were found guilty of breaching the league's financial rules.
City have denied all wrongdoing and appealed the decision.
The win preserved City's perfect Premier League start and moved them three points clear at the top ahead of Wednesday's Champions League clash at home to PSG.
"After we were very happy on the pitch, sharing time with our fans. Probably it has been more tough for our fans than for the players or for me," Maresca told reporters on Tuesday.
"It is more complicated because if I was an Arsenal fan or United fan and you are a City fan, I can say, 'My friend, you are a cheat' or these kinds of things. So probably, it has been more tough for them."
Maresca also hit back at criticism of City's celebrations on the pitch at Anfield, with the Italian coach saying he could not understand why they were being questioned by some media and other fans for enjoying a significant victory over their rivals.