"If multiple papers are accepted for presentation, each paper requires a separate registration fee." -> Why?
For most conferences, the primary costs are:


Venue
Catering
Society fees
Program and proceedings
Keynote / scholarship travel sponsorship


The price of these is wildly variable depending on the arrangements that have been made.  At the low end, consider a conference using university meeting rooms, asking people to go out for lunch on their own, using volunteer labor and keeping program and proceedings electronic.  This can be extremely cheap, on the order of a couple of dollars per attendee, even for a rather large meeting.  

When a conference meets in a hotel, the expenses go up like crazy.  For a week-long conference in a major city hotel, the venue and catering expenses can easily run as high as $500/person.  These are often required to be booked far in advance, based on the number of people expected to register for the conference, and there may be limited flexibility to change these numbers if attendance falls short.
Hotels also frequently ask a conference to have attendees book in the hotel, and will ask for "insurance" from a conference in the form of a commitment to get at least a certain number of rooms booked and to pay for unbooked rooms if the conference falls short of that commitment.  This can add thousands of dollars of expenses.  These factors can operate at universities too, which sometimes demand high venue and catering fees even when their own professors are organizing.

With an expensive venue, then, a conference's organizers can thus get very nervous about whether they will have enough money to cover their anticipated expenses, if registrations are less than anticipated.  This is especially the case if the conference has had difficulty meeting its expenses in the past, and may be in trouble with its sponsoring society as a result.  

Forcing people to register per paper is one response to trying to avoid this type of shortfall.  Not only is there the fee, but if you're registering a second time, you're more likely to send a second person from the group, who will likely have their own hotel room.  For a conference that may be facing a shortfall in its hotel commitments, a single registration easily can be worth $2000 in increased income and decreased hotel penalty.

Personally, I still don't approve: I think that a conference operating at such a razor's edge would do better to take other approaches to trying to make up its budget shortfall.  I can understand, however, why the organizers of respectable conferences sometimes choose to do it: it's not that they are getting rich, but that they are trying to keep from going bankrupt while they make their venue rich.