Twelve people were killed by brothers Said and Cherif Kouachi at the French satirical magazine's offices last week, with the gunmen reportedly yelling, "We have avenged the Prophet" while carrying out the attack.
While Toure -- a Muslim himself -- advocates freedom of speech, he feels news outlets also have responsibilities.
"As a Muslim I always believe in the way people can say what they want to say," he told CNN's Amanda Davies.
"But for me, the most important thing is that we know something that sometimes the newspaper is doing a lot -- and they're trying to do too much, and sometimes they do it not with respect."
"Everybody has his point of view -- everybody has something to say about that," Toure added. "Of course it's a newspaper trying to say something. But sometimes it hurts people."
Depicting Mohammed is offensive to many Muslims and the magazine's past cartoons of the prophet apparently motivated the attackers in last week's slaughter.
The City midfielder says he was disappointed to hear of the attack on Charlie Hebdo -- and he now fears for the safety of his Muslim friends in the French capital.
Currently on international duty with Ivory Coast ahead of the 2015 Africa Cup of Nations which begins this week, Toure spent a season playing in the French Ligue 1 with Monaco in 2006-07.
"When you hear something like that it's a bit disappointing," he said, referring to the attack on the Charlie Hebdo office. "I feel very sorry for the families -- they lost their friend, father, or their husband, you know.
"Of course I have a friend in Paris, I have people who I work with. You get a bit confused, a bit afraid, because, as a Muslim, I have a friend and they are Muslim as well and I'm afraid of what is going to happen."
The latest Charlie Hebdo issue has also been highly controversial, largely because on its cover is an illustration of a tearful Prophet Mohammed, holding up an "I am Charlie" sign accompanied by the words "All is forgiven."
The new cover was met with mixed emotions -- with some calling it a bold example of free speech and others criticizing it as needlessly offensive to Muslims.