Intrinsically, smaller organisms have fewer recovery mechanisms when compared to multicellular organisms. So, it kind of makes sense for them to be more susceptible to radiation.
At the low level, it boils down to the amount of energy an organism has at its disposal: prokaryotes have no mitochondria and thus cannot usually form multicellular organisms. If radiation hits an prokaryotic organism (i.e. a single cell) - it's alone by itself and probably well gone after the hit.
If radiation hits an eukaryotic (multicellular) organism, it still is able to compensate for that (to some degree) and still remains in the breeding pool for some time after the event.
The key difference between the two is the ability to reproduce itself after the damage.
