Verified answer

Originally, Ubisoft wanted to make a Prince of Persia game based on the hashashins. When they started writing, they noticed that they had enough ideas to make a new IP based on the hashashins, without having links to Prince of Persia. So they created Assassins Creed. The first game, which shows the real hashashins who actually fought the Knighs Templar. So they decided to make the templars the antagonists. In real history, hashashins and knights templar dissapeared a long time ago, so the fiction behind the game is that the war between the assassins an templars continued through the ages.

Assassin's Creed was actually meant to be part of the Prince of Persia series. As the game developed, the developers realized that the game was too realistic and historical to be part of the magic-ridden Prince of Persia line of games. This is why you see the free-running and assassination elements of PoP in Assassin's Creed today.

When they changed the game, the Templars were always the antagonists (enemies). They simply changed the main characters into the Assassins. I hope that clears things up.

Because the First Game was set in the era where the "Knights Templar's" existed,

they continued to use the templars as the antagonostic team.

as for why the assassin's where chosen as the protagonist team..i have no clue.