Speaking at the Arab World Institute in Paris, Hollande said: "It is Muslims who are the main victims of fanaticism, fundamentalism and intolerance", adding the whole country was "united in the face of terrorism."
The Muslim community in France, Europe's largest, have "the same rights and the same duties as all citizens" and must be protected.
The five burials included those of two of Charlie Hebdo's best-known cartoonists, as the satirical magazine continued to fly off the shelves, sparking fury in some parts of the Muslim world for depicting the Prophet Mohammed on its cover.
After the shooting at the magazine, which killed 12 people, the French rushed to get their hands on the "survivors' issue" which sold out Wednesday before more copies of an eventual print run of five million hit newsstands.
Also Read
Long queues formed throughout the country again on Thursday as copies again quickly ran out.
"Charlie Hebdo is alive and will live on," Hollande said yesterday. "You can murder men and women, but you can never kill their ideas," he said, declaring the previously struggling weekly "reborn".
In all, 17 people died over three days in the bloodiest attacks in France in half a century, which ended when commando units stormed two hostage sieges and killed all three gunmen.
In yesterday's new edition of Charlie Hebdo, the prophet is depicted with a tear in his eye, under the headline "All is forgiven". He holds a sign reading "Je suis Charlie" (I am Charlie), the slogan that has become a global rallying cry for those expressing sympathy for the victims and support for freedom of speech.
Millions rallied in support of free speech after the assault, while French prosecutors, under government orders to crack down on hate crimes, have opened more than 50 cases for condoning terrorism or making threats to carry out terrorist acts since the attack.
They include one against controversial comedian Dieudonne, who was arrested Wednesday over a remark suggesting he sympathised with one of the Paris attackers and will stand trial.