It's not a mass conspiracy, but it might as well be. By publishing results that suggest X is bad for you, academics are able to solicit more funding -- and they are always trying to obtain more grant money. Similarly there is money to be made selling "natural" products, so organizations that market homeopathic / holistic / natural goods will fund academics to do more studies. Look at eggs, they were bad, now they are good. Now it seems trans fats are the latest problem. I take the approach that if it's encountered naturally, it's more than likely something our bodies can deal with (I guess radium is a notable exception).
As for me, as an example, I buy organic milk, but more because I am hoping the cows are treated better. There are very good reasons to distrust our government as far as products which are marketed despite known cancer risks (any meat with nitrites come to mind). It is true that pharmaceutical companies will market less effective compounds in order to gain income from royalties, royalties which would be unavailable from a compound which is readily available say within certain foods or herbs. Still doctors have been coming across real problems from herbal remedies doing nasty things like causing heart damage. So much for "natural" chemicals.