Over the past few days visitors to the site have reported virus infections on their Windows machines caused by an exploit in the Acrobat PDF reader browser plugin.
There have been no public comments from YoYo Games on the issue. Although YoYo Games is a bespoke site the makers of Game Maker have a history of using out of date software which has been exploited on more than one occasion in the past.
Update (~12:35 BST): At around the same time as this post was initially written YoYo Games made a post about the matter. Russell Kay writes that the problem was caused by an attack on the OpenX ad server which was used to manage the advertisements displayed alongside games on the website. The ad server has now been removed with ads being served directly from Google and it appears that the issue has been resolved.