Some schools want more information from you that aadsas could not provide them and that is why they give you secondaries. All the schools that do not have secondaries also have similar fees.
The $$$ is used to pay the admission staff, secretaries, etc...
Some schools are really ethical; meaning that they only collect the fees after your application has been processed you will be contacted. But other schools just want you to send them a check. Say 4k students apply to school may be like at least 500 people wont even hear back from them... But they still suck the money out of the bank account. thats what happened to one of my buddies.