According to Rabbi Rafi Feuerstein, who is completing a Master's Degree in psychology, the sources of the conflict are that
Part of the problem, I think, is simply that rabbis have taken on a role they are usually completely unqualified for and should not be filling. Rabbis can be very wise men but, unless they are trained, are not social workers and not psychologists and should not be offering people in real trouble help in most of the areas over which, according to Feuerstein, the majority of the conflict with the psychologists takes place ("issues related to the children's education, problems in the family, troubles between husband and wife, individuals who have difficulty finding their place in their community, people feeling they are experiencing a non-clinical breakdown"). On the whole, they should stick to questions of a halachic nature.
"The psychologist is obligated first and foremost to the patient, while the rabbi is obligated first and foremost to the patient's God. The psychologist tries to help the patient solve his problems by helping him to connect to himself, while the rabbi tries to help him by helping him connect to the world of mitzvot [righteous deeds]."
The greatest concern of the rabbis stems from their assumption that psychologists, who are free from the bounds of halakha (Jewish law) and obligated only to alleviating the distress of their patients, grant legitimacy to phenomena and behavior that are proscribed by halakha...
The rabbi's suspicion vis-a-vis the psychologist is further reinforced, said Feuerstein, by the fact that many rabbis view the psychologist as a competitor - as "someone who can hurt the rabbi's ratings among the public" - who can impair the rabbi's standing as the leader to whom the members of the community present their problems.
In addition, the whole point of going to see a psychologist is to work out for yourself what you really feel and want through talking to someone with no emotional involvement or vested interest. A good psychologist is someone who can put their own baggage aside and help people come to their own decisions; not to guide them, but to help them guide themselves. If someone really wants to find a solution to their problem which is in tune with halacha or with a religious way of life, they will through the psychologist (it would, of course, help if the psychologists had a better understanding of where their religious patients are coming from -- another important problem highlighted by the article). What the fear of psychologists betrays is a fear of what would happen if members of the religious public thought for themselves and expressed their true desires.