A couple of questions come to mind
1. Who paid for the study and what kinds of controls were used?
2. Were people recruited for the study at random in order to try Transcendental Meditation?
If the participants were just people who self-refer then they are likely people who believe that TM is desirable to learn - but TM is marketed to people being willing to pay thousands of dollars to learn 'special' techniques which the proponents of TM claim may give them 'special' powers (like the ability to fly). Please copy and paste this into a browser --> youtube.com/watch?v=NHwhGUo90jw
Such people should not be considered a random sample of typical people and so their results would not represent what one would expect from the average person who just wants to learn 'standard' meditation and hatha yoga at a local studio (perhaps for some of the scientifically demonstrated benefits referenced in Smiley's post).
Therefore
1. They must recruit disinterested parties and pay them for their time.
2. The study should be peer-reviewed by social scientists, a preponderance of whom should agree that the stated conclusions of the study can be reasonably inferred from the data gathered during the study.
If both of the above hurdles are cleared then we must accept the results of this one study and then ask ourselves if said results should outweigh the "large body of research" gathered "over a period of 25 years" which is referenced by the United States Government's Office of Alternative Medicine (nccam.nih.gov) especially since TM and the claims made by its proponents are atypical.
After all, would yoga and meditation have become as popular as they are in the West if they wrecked such havoc upon the vast majority of people who practiced them?