When the allegation is of a serious nature - which any accusation of racism undoubtedly is - it is only right that an appropriate standard of proof is applied (beyond reasonable doubt). When it comes to verbal assaults, it is not just the mere utterance of a word(s), but the context in which it is said. From what's been reported, and as is obviously implied by the not guilty verdict, there was doubt as to whether Terry directed the words as an insult. The correct decision was made.
As a matter of principle, I don't think the FA should investigate any allegation of racist abuse using their much lower standard of proof (the balance of probabilities), but as we know only too well, they have set a precedent with the Suarez/Evra case and I think it would be unacceptable for them to not now carry out their own investigation.