@omellet
You make an interesting point. The patent office doesn't really encourage the filing of patent applications though. Instead, it examines patent applications after they are filed.
Their point is that the Patent Office would have a "perverse incentive" to encourage/increase the number of filings and the numbers of patents it grants if the Office were allowed to keep the proceeds raised from fees, which you correctly point out is not the case right now.
@wavefunction.
I see their point, but I don't quite follow their logic. I don't think the patent office has much control over how many people file patent applications, they just examine them once they are filed. For example, the patent office doesn't advertise during the superbowl. If they have less resources to examine the filed patent applications, then they will not be able to examine them as effectively.