You can't transfer ebooks to your Kindle from your computer if it is messed up with viruses or a big fat trojan (software that sneaks viruses into your machine disguised as something nice).
Make yourself lower risk by being careful what you click and what web sites you visit. If it sounds too good to be true... trust me.. it is on the Internet. Lately I have heard from two people (two too many) who got sucked in by a scareware program called System Tool. Basically it weasled its way onto their computer from an infected website or infected email (not sure which). The software comes up saying "your computer is infected, let me check it for you," then wants $$ to clean up the "malware and viruses" for you. Everything about this is bogus. If you see anything like this, make a note of the name exactly, then do a google search to find out how to get rid of it. If you don't feel comfortable doing it yourself, it would be a good idea to take your computer to your local PC doctor and let a professional clean it up for you.
Stay SAFE!