This study was mainly by religious people. The author is a firm believer that prayer on the part of the patient is beneficial, and he works at the Beth Israel Deaconess Medical Center (a combination Jewish and Methodist hospital). And two of the participating hospitals were Baptist.
I do think this controlled study gave strong evidence that third-party prayer does nothing. However, other studies do show that prayer on the part of the patient does help. On the other hand, so does meditation. It's not about a deity helping a recovery, but about the mental state of the patient. The mental state of the patient is a known factor in health care, and both prayer and meditation put the patient in a mental state that helps recovery.
So in the end, go ahead and pray. It can't hurt, but prayer on the part of the patient does help.