The money that gets paid to the patent office when filing for a patent mostly goes to keep the patent office going.
The patent office is not really a for profit business, they just make you pay fees when you file stuff with them to cover the cost of the work they are doing. Bureaucracy costs money and rather than making the average tax-payer pay for it they charge the people who directly benefit from it.
You can see what the US Patent Office charges here:
https://www.uspto.gov/learning-and-resources/fees-and-payment/uspto-fee-schedule
You can also see what their budget is here:
https://www.commerce.gov/sites/default/files/2022-03/FY2023-USPTO-Congressional-Budget-Submission.pdf
The have some money over after paying of everything, but they also need to keep some money in reserve to cover next years expenses in case they take in less in fees.
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