If it was a straight scene you probably wouldn't be asking that at all, or give it a second guess. Many people forget Gus Van Sant is in fact, gay.

However the sex scene in the film was actually Lukas Haas' idea, who wanted his character to be sexually ambiguous. You can see him talk about it on the DVD. Much of the film was improvised. In fact, the yellow pages salesman was an actual salesman who wandered onto the set trying to sell orders.