Images stabilized on the retina (say, for example any opaque elements on a contact lens) quickly become invisible. Our visual system relies on very rapid, continuous, small eye movements that constantly change the position of the image of the external world on the retina. A contact lens display, on top of every other technical hurtle, would have to compensate for this in a way that the visual system could readily interpret. It would also take a lot of practice to get used to display elements displaced from the exact center of your vision that you could never move your eye to focus on (like trying to get a better look at a 'floater' in your eye that keeps moving away).
And of course there's also, "CEASE FIRE! CEASE FIRE! . . NOBODY MOVE, I LOST A LENS"
It's one thing persecuting people for their religion but persecuting atheists is going too far.
A small minority of 'different' people in your community often makes people uncomfortable when part of the culture is professing just how right and good it is to agree and identify with the majority. When that minority attempts to become vocal they are by definition wrong and therefore it is justifiable to punish them. If all you have to prove that you're living your life correctly is the assertion by yourself and those around you that it is so any argument against what you believe is dangerous. Certainly authority figures (from politicians to parents) won't allow dissenting opinions to spread, like some horrible disease.
People aren't persecuted for their religion. They are persecuted because their religion (or ethnicity or social status or etc.) is different from the majority of those around them. Group-think and ignorance will attack what it doesn't understand or can't control in whatever form it takes.
One could argue that, historically, atheism is the most persecuted belief system still in practice. It would explain the relatively small proportion of the population that atheism makes up, as well as why that small proportion is spread throughout the world with no great central region to call home.
The flow chart is a most thoroughly oversold piece of program documentation. -- Frederick Brooks, "The Mythical Man Month"