He was speaking a day after the satirical weekly's publication of a cartoon of the Prophet Mohammad sparked violent clashes, including deaths, in some Muslim countries.
Demand has surged for Charlie Hebdo's first issue since two militant gunmen burst into its weekly editorial conference and shot dead 12 people at the start of three days of violence that shocked France.
The magazine's distributors said that its print run had been lifted to seven million copies, dwarfing its usual circulation of only 60,000.
A cartoon image of Mohammad on its front page outraged many in the Muslim world, triggering demonstrations that turned violent in Algeria, Niger and Pakistan on Friday.
"We've supported these countries in the fight against terrorism," Hollande said during a visit to the southern city of Tulle, traditionally his political fiefdom.
"I still want to express my solidarity (towards them), but at the same time France has principles and values, in particular freedom of expression," he added.
The shootings in Paris were prompted by Charlie Hebdo's previous publication of Mohammad cartoons, a depiction many Muslims consider blasphemous.
Police in Niger fired teargas on Saturday at hundreds of rock-throwing protesters in a second day of clashes over Charlie Hebdo's publication of the image.
A police officer and three civilians were killed on Friday in the Zinder, the second city of the former French colony, while churches were burned and Christian homes looted.
Protests also turned violent on Friday in the southern Pakistan city of Karachi where police used tear gas and a water cannon against demonstrators outside the French consulate.
A photographer for French news agency Agence France-Presse was also wounded by a gunshot during the protest.
Several Algerian police officers were injured in clashes with demonstrators in Algiers after rioting broke out at the end of a protest.
"There are tensions abroad where people don't understand our attachment to the freedom of speech," Hollande said. "We've seen the protests, and I would say that in France all beliefs are respected."
Produced by survivors of the attack on the newspaper, the latest edition of Charlie Hebdo sold out in minutes when it hit newsstands on Wednesday. It shows a cartoon of a tearful Mohammad holding a "Je suis Charlie" sign under the words "All is forgiven."
A lawyer for one of the gunmen in the Charlie Hebdo attack said the man had been buried in the eastern city of Reims in an unmarked grave so as not to attract admirers.
(Additional reporting by Gregory Blachier Editing by Jeremy Gaunt)