Having negative piety gives you a bonus to technology rate and taxes, which is how you get the tech rate. There is no unmentioned bonus. Ideally you want to keep piety at one end of the spectrum or the other, both have advantages. Piety is not like Piety in crusader kings, where it is all good. Instead it represents the advantages of secularism (tech, church taxes) versus theocracy (morale and stability).
You can see your current modifiers by hovering over the Current Piety label or percentage slider on the Religion tab. Hover over the flag icons on either end of the slider to see the maximum available modifiers.
