The FDA approves consumption of many things, however they also set limits of recommended amounts and state that exceeding certain amounts of things can be detrimental to your health, that is their job. For example, it is safe to take NSAIDs to relieve pain and inflammation, however if you abuse the product you can suffer liver damage, develop ulcers and cause other problems to your body. You can take Viagra as a safe product also but beware there is a 14 page disclaimer stating that if you take it, any one of a myriad of medical maladies may occur to you as well including death.
This taken from email conversation with Bio-chemist at Birko corp:
"One thing you do need to be aware of is that Fermcap S is a silicone based antifoam (dimethyl poly slioxane). Birko sells a silicone based antifoam to brewers (Birko AF100) however we strongly discourage its use in beers that are not clarifies by filtration or centrifugation. The FDA has limits on the amount of this material that is allowed in food. Here is a comments from Dana that was posted on a probrewers forum:
"Brewers should not use silicone-containing antifoam for unfiltered beers. The FDA allows active silicone to be used up to 10 parts-per-million (ppm) but stipulates that the silicone must be removed prior to packaging by either filtration or centrifugation. In the case of unfiltered beers, use a food grade, non-silicone antifoam."
I'm not trying to dissuade people from using Fermcap, in fact I use it when necessary. The information I stated is not shenanigans and if you do a basic internet search you will in fact find a ton of articles on brewing forums and published articles repeating this information as well as other products that can be used as substitution.
The fact remains that if used beyond the limits stated by the FDA it should be filtered out. In addition, some people are just really against putting these types of products in their beer so they should be educated.
As with anything, if used as labeled there should be no problem but lots of people do not read labels or follow directions and think that if a little is great a lot is better. As a home brewer using 1-2 drops per gallon I am not concerned but in a larger batch setting or commercial application I can understand the concern and limits set forth.
I know people that use it in their starter, then in the boil and then again in the fermentor for example and IMO that is complete overuse of the product and if that is their routine for each and every batch of beer they brew, then yes, I would be concerned that over time they are over exposed to the product.
Just my .02