The most common way get Ability Points is through leveling up. Every time you level up you get one new point to spend, and even after reaching your maximum level of 40, you can continue to 'level' for more ability points by gaining more XP.
There are also Ability Points you can earn at certain locations. Every Tomb has an Ancient Tablet that can be read for one Ability Point.
Completing a Hermit Locations by resting in the right place grants an Ability Point.
Finally, killing a war elephant in a Roman camp (ie not during the main quest) grants an ability point.
