PCRM does have its critics.
No, they are not a front for PETA. They have two main areas that they work towards: (1) promoting healthier lifestyles through increase of eating fruits, veggies, etc. and (2) reducing medical animal testing.

It is the second of the above categories that draws the PETA comparisons. They are not fanatical like PETA. Their point, as a bunch of MDs, is that much of the medical testing done on animals is unneccesary and unhelpful. Not that there should be no medical testing - just that medical institutions and pharmiceutical companies value the animals' lives and not view them just as you would a test tube or the like.

THe NY Times article (if its the same one you are referring to) also was a reaction by Atkins to PCRM's bringing to light Dr. Atkins' own health problems. Most of the disparaging things said about PCRM in the article were quotes from the Atkins organization. For instance, they said that the majority of the members of PCRM aren't even doctors so the "physicians" in their name is misleading. That statement is misleading. The leadership of PCRM is made up of almost all doctors (some PhD's and dieticians also). The "members" are people like me who give them $25/year and get their newsletter. The credentials and affiliations of the board of the PCRM is pretty impressive. The president of PCRM is Dr. Neal Barnard who has published many books on health and nutrion. I have read a few and they were well done. Others are Dr. Caldwell Esselstyn, a well known Cleveland Clinic Cardiologist, Dr. T. Colin Campbell of Cornell University who has published a number of studies on the health differences of the diets of the Chinese vs. what Americans eat, Dr. Andrew Weil of the University of Arizona Center for Integrative Medicine and Dr. John McDougall who is an MD specializing in nutrition and weight loss.

You may want to read some articles on the PCRM website and some of the studies they are involved in before you condemn what they stand for.