They persecute non-Muslims with the intensity they persecute all dissidents. Here's an excellent piece by Paul Marshall in the Weekly Standard:
[The 1991 document] …outlined a plan gradually to choke the Baha'i community. They were not usually to be subject to further arrests or deportations from the country: Henceforth the government was to ensure that "their progress and development are blocked." They could be enrolled in schools but only if they "have not identified themselves as Baha'is." They were to be expelled from universities altogether. They could have jobs only on condition that they not "identify themselves as Baha'is," and, if employed, must have only "a modest livelihood" and be denied "any position of influence." Khamenei added a handwritten note to the directive expressing his approval, thus conferring on it the status of an official decree. (These and other documents have been made available by the Baha'i community--see news.bahai.org.)
The regime continued to persecute the Baha'is, as well as other religious minorities, and parts of this plan were carried out--including their exclusion from universities and many jobs. But now the government's program has entered a more intensive and systematic phase. An October 29, 2005, confidential letter sent on Khamenei's instructions by Major General Hossein Firuzabadi, chairman of the Command Headquarters of the Armed Forces, ordered the Ministry of Information, the Revolutionary Guard, and the Police Force to "acquire a comprehensive and complete report" to identify all Baha'is.
(Hat tip: Norm.)