For the last week, every time I go online I get annoying pop-up ads and warning messages sayying' you're computer may be infected with malware and viruses, click here... " . Also, one of the pop-up ads is a virus scan. When I try to close them, I have to click close about ten times to get rid of them all. Is this a virus? I disabled all add ons, and have done a scan with antiver, but it's still happening.

Sounds like you ARE indeed infected with some nagware, possible Antivirus XP.

Give Malwarebytes a run through your system.
This should remove this issue.

This happened to my friend midway through the semester. It was a virus and would pop up saying the computer was infected and to go to such and such website to buy the antivirus software. DON'T DO IT, if you didn't already guess. It took her a couple of different REAL antivirus programs and debuggers before she got it MOSTLY fixed. Might want to go pro on this one, unless you can follow the manual instructions that it seems only programmers would know how to follow. Best of luck.

Here's what you need to get and keep your PC clean:

AVG Free antivirus (viruses and trojans)
Lavasoft Ad-Aware Free (adware and spyware)
Spybot Search & Destroy (adware and spyware)

Make sure you get the right version of Spybot - there's an imposter out there (I've provided the link to the correct one). Note that you want the Ad-Aware free version on the left, unless you want to complete an offer to get the Plus version on the right. I recommend both Ad-Aware and Spybot since in my experience they can find different things.

In addition to running the above weekly, make sure you never open an attachment in an email without scanning it first; turn off HTML display in your email client; and use Firefox for everyday browsing rather than Internet Explorer (only use Internet Explorer for Windows updates and those few sites that require it). Turn on your Windows firewall in XP or Vista.

Do all the above and chances are you'll be a happy camper.