Ever since its debut title, Assassin's Creed has become known for its war between the Assassins and the Templars. Throughout the history of humanity, these two groups have clashed over ideologies and squared off on literally every continent in the pursuit of their goals. Numerous and significant blows have been exchanged by both sides over the years however, at their cores, they pretty much share the same hope for the world: peace.
Whilst the Assassins believe in peace through freedom and liberty, the Templars are a bit more grey when it comes to pursuing an end to tyranny and injustice. Often a lot more brutal in their methods and, more often than not, prone to a fair amount of corruption, The Templar Order believes in peace through order, control and direction from above.
Nevertheless, with so many games, characters and history behind them, it's inevitable that sometimes the good guy/bad guy roles get changed up a bit. Just because players mostly see things from an Assassin point of view, doesn't necessarily mean that is view they should take as gospel.
There are many examples of Templars with nobler goals, more ambitious and logical plans, or those a bit more clued up than their Assassin counterparts.