bump, i need to know this too, cuz ive had people swear that clear cups are bad and kills roots and blah blah, but ive had others that showed me pics that proved that wrong, so iono.
Light will damage roots, no doubt. You're plant may survive, but it will be stressed and may be male or turn herm. Best just to put that cup inside another opaque one or wrap it in duct tape to protect the roots. Cups are cheap. Why take the chance?
If you are using clear because you want to see the roots somebody started a thread where he used clear cops then stuck them inside red cup to protect the roots, that way he could see the roots.
clear cups are OK as long as you transplant the minute you see a root. but if theyre just for starting, that's cool. i know cats who clone in clear cups so they know when the roots have formed.