Currently, flying with pot is taking a chance, even for those that have a medical marijuana card; if the medicine is discovered by the TSA, they can take it away.
Although it is not technically legal to fly with pot (airports are federal property), TSA policy suggest that passengers who travel between states in which they can legally use pot may be allowed to fly. So if the passenger has authorization to use medical marijuana, or is flying between Washington and Colorado, where possession of the drug for recreational purposes has been legalized, local law enforcement may not intervene.
From the TSA website:
"TSA security officers do not search for marijuana or other drugs. In the event a substance that appears to be marijuana is observed during security screening, TSA will refer the matter to a law enforcement officer.
Whether or not marijuana is considered “medical marijuana” under local law is not relevant to TSA screening because TSA is governed by federal law and federal law provides no basis to treat medical marijuana any differently than non-medical marijuana.
Even if an item is generally permitted, it may be subject to additional screening or not allowed through the checkpoint if it triggers an alarm during the screening process, appears to have been tampered with, or poses other security concerns. The final decision rests with TSA on whether to allow any items on the plane."