Are satoshis fungible?

The answer is complicated.. At the most basic (most important) level, the answer is yes. Every satoshi can be used to pay miners for the valuable ledger and time stamping services of the protocol.

At a human level, the honest answer can only be no. Just as people have always discriminated against the source of their gold, diamonds, or dollars .. Choosing to do business with some people and flat out refusing others (drug money, Nazi gold, blood diamonds, etc). Bitcoin brings even more transparency to the history of any particular unit of money, and absent some force telling people they have to accept all satoshis as equal, they simply may not.

Satoshis do have one key advantage - on a protocol level they will always be perfectly fungible and I can foresee no situation in which that would change. As demand for blockspace increases, this necessarily also increases the fungibility of satoshis by increasing the percentage of trade which cannot prefer one satoshi to another.