Pop-ups are usually caused by one of the following situations
Page re-directors: - usually a piece of malignant software downloads from an infected website which usurps the normal web browser start up page.
It will change the web start -up page and worst it will prevent you form resetting the page to your usual start page. In some circumstances install hidden software which ensures that it will re-install even after removal, making it very difficult to successfully remove.
Bogus Virus Warnings: - another form of pop-up, usually requesting you to purchase a full version of the application to fix the problem. 
Never try to purchase the suggested software as in many cases once they have your card details they are either used for a shopping spree or sold via the Internet to various nefarious characters.
Beware some of the latest malware locks your system and will only be unlocked by payment of a ransom. It encrypts your hard disk and can only be unlocked by paying the ransom.