The issue here is not whether all genetic modification is safe, it is about the misleading reporting of a scientific article. The scientific community do have ethical concerns about safety, which is why such studies are performed in the first place.
In this particular instance, they were screening for toxins that could be produced in error by a sequence. In the particular gene they were looking at (one commonly used to promote expression of proteins for another inserted gene), they couldn't find any. This doesn't automatically make it safe, but it rules out a set of potential issues.
And remember, such allergens/toxins can be produced in non-modified organisms, which is why we even know about them in the first place.