How often does a cosmic ray hit our eyes when we are on Earth? Astronauts often see flashes when they are in space. How often these particles  make their ways down to the Earth and hit us? What's the chance they hit our eyes and see flashes?
 A: Muons are the main cosmic rays reaching sea level with a possibility of interacting with matter. Neutrinos interact very weakly and need special detectors to be seen at all.
Rule of thumb when I was working with counters is that the flux of muons at sea level is 1 per cm^2 per second, wikipedia gives this number for over 1 Gev 

The number of particles that hit the ground is dependent on several factors including location with respect to the earth's magnetic field, solar cycle, elevation, and the energy of the particles. For 1 GeV particles, the rate of arrival is about 10,000 per square meter per second. At 1 TeV the rate is 1 particle per square meter per second

...

When cosmic rays enter the Earth's atmosphere they collide with molecules, mainly oxygen and nitrogen. The interaction produce a cascade of billions of lighter particles, a so-called air shower.[12] All of the produced particles stay within about one degree of the primary particle's path. Typical particles produced in such collisions are charged mesons e.g. positive and negative pions and kaons. These subsequently decay into muons, which are able to reach the surface of the Earth, and even penetrate for some distance into shallow mines.

For energies above 1 GeV see this link.
The question then becomes biophysical, can the eye  detect ionizing deposition which lasts much less than a second as the velocities are very high? The answer is no, unless there is an interaction with nuclei in the eye and there is a shower in the eye. The flux at sea level is predominantly muons  which interact weakly with nuclei so there is very small probability that a shine in the dark is a cosmic interaction. 
In the stratosphere and where the astronauts are living the flux is composed mainly by hadrons, and those have a high probability of interacting with nuclei in the eye.
