I keep getting a pop up saying, congratulations iPad user' saying I have won something. I have tried hard reboot, I have factory reset my iPad and still I get the pop up.
You are most likely are accessing/have accessed a sketchy site which has opened a malicious site in a different tab. Sadly, you have not won anything (although a nice cruise to the Bahamas would be nice/$50 Amazon gift card). Try clearing out all of the tabs in you internet browser.
Also take a look at this page about phishing from Apple.
Additionally take a look at this amazing post over at Apple Support Communities
Note: Browsers within apps can are still susceptible to this. They use WebKitView (basically Safari inside an app). In this case just close the popup and the webpage within the app. Try not to access the page or section your were accessing in that app.