The room clerk, played by the movie's screenwriter Buck Henry, is at the Taft Hotel when Benjamin arrives to book a room for his affair with Mrs. Robinson. The clerk immediately catches Ben off-guard Benjamin by asking him, "Are you here for an affair?" But he's talking about a social gathering; the Singleman Party going on at the hotel.
Basically, the clerk provides Ben with some opportunities to act comically awkward. He not only acts strangely when he thinks the clerk is asking him if he's there to have an affair, but also when he talks about getting his luggage out of his car—really just a toothbrush.