It means just what it says. That when debating a subject (politics is a great example), people can have differing opinions, and a well-functioning political system includes a sense of respect for those who have different opinions.
But people should not form opinions based on made up or fraudulent facts."I may disagree with what you have to say, but I shall defend, to the death, your right to say it."
If the economy is poor, people may have differing opinions on the best way to improve it. But if one person argues that the "facts" say the economy is fine while another says it is hurting, then only one person is truly operating with the "facts."
Hence, during an argument about the economy, say when some new economic numbers are released, one side may say to the other that they are entitled to their own opinion, but not their own facts.