On September 21, 2011 the BATFE issued an open letter to all Federal Firearms Licensees. It essentially states that anyone who lives in a state that recognizes medical marijuana use and who holds a "card" is an "...unlawful user of or addicted to any controlled substance...".
While individual states have decided to recognize the medicinal value of marijuana, the fact is that it's still a Class I controlled substance according to the Controlled Substances Act. Class I drugs have a high probability of abuse and have no medicinal use according to the CSA and are, therefore, illegal.
When answering the questions on the 4473, anyone holding a red or MMJ card is required to answer "yes" to question 11.e. The transaction stops right then and there.
According to the open letter, people who hold a "card" may not purchase nor possess firearms or ammunition.
Whether right or wrong, that's the way it is.