It is late and my brain isn't functioning 100%, but yes surges from lightning strikes can and will damage electrical components, especially semi-conductors. Just a few pictures below I found from the internet show some possible damage in a computer.
While you are correct in that there are a lot of protections in place in the electrical system to prevent damage, transients (short lived changes essentially) due to power outages/surges, lightning, electrostatic discharge (ESD), etc. can be very difficult to protect against in all situations.
Most components have an absolute maximum rated voltage that can be applied to it. Exceed this and you may have a latent issue that will show up years down the line, or immediate destruction. Lighting for example will introduce an extremely large transient that will destroy pretty much any component not specifically designed to suppress lightning. Transient voltage suppressors/protectors are generally used for protecting against ESD and lightning up to a rated level (standardized) and generally use the properties of various electrical components to create a low resistance path away from the sensitive electronics.
The wikipedia page on
Surge protectors is actually not too bad and provides a starting off point I suppose. Of course I'm assuming some basic knowledge of electricity here.
Feel free to ask any questions or whatever, even over PM! I'm probably halfway incoherent since it is past my bed time, but I'll be happy to respond tomorrow.