It seems like cleric in PF can use unlimited times of 0-level spell a day.
By a simple calculation, a level 1 cleric working for 8 hours a day can create 9600 gallons of water a day, by using the Create Water spell.
Am I misunderstanding the rules or is that how the Pathfinder rules work?
If a cleric can provide water for a whole town of people in a desert, this will surely bring a huge effect on desert civilizations. I am not very familiar with the worlds and settings of Pathfinder, did the designers consider these types of things when making the setting?
In short, yes.
Your numbers are correct. A level 1 cleric can cast 4800 cantrips in 8 hours, which would make 9600 gallons of water, just like you say. It's definitely true that a civic-minded cleric could totally solve the water problem for a mid-sized city. If you've got a backup cleric or two, or are willing to take a risk on occasionally not having water for a time, this is a totally reasonable way of generating water.
Your secondary question about how this would effect a desert civilization: You're probably right that the existence of this kind of magic should have a huge effect on how desert civilizations survive and thrive, but generally D&D and Pathfinder setting books don't actually go into the realistic implications of magic. The economics on D&D and PF make absolutely no sense at all, and this is just another branch of that nonsensical tree.