There are a great many reasons why this occurs to perfectly fine sites. To start off with - I was happy to see the site was back up and running. Earlier in the day I was a bit disappointed as the site was taken down and I was looking forward to see some great new creations.
Anyway - as a software engineer with a primary focus in web application development - there are a great many reasons why this occurs. We have had to deal with this with the company I work for, and it is quite frustrating.
First and foremost - a lot of browsers and virus softwares look at reliable sources for any potentially unsafe sites. This is why some browsers and virus software set off red flags. If google marks a page as potentially unsafe, they are considered a "reliable" source.
Now - I noticed that the "issue" was not presented in this thread yet, so I cannot expand on what actually happened here, but the top 5 reasons why this occurs: (please note, this is for people who have their own sites and can be helpful. The fantastic administrators have already resolved the issue here :good
1. Code spoofing (Someone interjected network code when perhaps a google crawler was reading data setting off an alarm) There is no way to avoid this unless a site went entirely through SSL.
2. Someone posts, has a link to, or provides some form of content that is related to another page which has been flagged as well. An example, my photos I host on my own web server. If my website got flagged as a result of code interjection, it is possible that this site would get flagged too, just because of an image.
3. An uploaded file has a threat within it. (Unlikely for this site as they are mostly images, but on other sites it can be a big issue)
4. Code interjection - Someone managed to interject code within the site. This is easily doable on sites that run on a database back-end and don't have safeties in place. Someone can type into say - a thread post box, and include code that would put something within the database, that when displayed on an html browser would cause issues. This is typically javascript. I will not attempt to demonstrate.
5. Third party software - This is a big one, though rare now as most people host things on their own servers now. Visitor counters, plugins, etc. that run on third party servers are an issue. If those servers get infected it can infect your own page, or be linked back and red flag your page. It is best to never run third party software that is on another server.
Now - the great part - there is a such thing as "too secure" and "too safe". I believe IAP was a victim of this. Google reported, as in the first thread post, that nothing whatsoever was found, yet it was flagged. IMO - flagging a site with 0 reported issues is not exactly in the best interest of the community. Then with virus scanners and browsers looking at sources such as google for malware sites and then reporting it to users would concern them. If my site that was responsible for my business which was dependent on sales - business would hurt... bad. I know that someone else in this community suffered from this. The worst part is Google just says it will take a couple days before it is rescanned and goes away - a couple days could mean big bucks.
Now that I am done educating and venting - stay safe, don't be fooled and turn great pens!