TechCrunch reports that AppGratis has not spoken publicly about the issue, but other apps have been pulled from the App Store for violating a rule on displaying 'Apps other than your own for purchase or promotion in a manner similar to or confusing with the App Store'.
However, TechCrunch notes that there are other reasons why the App could have been removed from the store:
That’s why many other scenarios are still possible. Maybe AppGratis uses a private API or breaks an insignificant guideline and Apple won’t put the app back in the store until an updated version is submitted. As always, developers are at the mercy of Apple’s review team. The team often contacts developers to require some changes to an app in order to stay in the store.
Paris-based AppGratis has coincidentally raised $13.5 million in January. With 7 million users and the ability to lead to up to 500,000 downloads for a single app, the company is not a newcomer. If Apple wanted to stamp out AppGratis, it could have done it a few months ago.
Update: Apple has confirmed to All Things D that AppGratis was removed from the App Store for using push notifications to send marketing messages, and also:
But sources close to the company say it was more than a little troubled that AppGratis was pushing a business model that appeared to favor developers with the financial means to pay for exposure. "The App Store is intended as a meritocracy," a source familiar with Apple's thinking told AllThingsD.