Where does the budget surplus of a conference go?
Here are some models I am aware of; combinations of these also exist:


There is a sponsor (e.g. government, local university or some academic organization) that covers part of the expenses but their rules for sponsoring are such that you cannot make surplus. You will need to return some of the sponsor money back to them so that the bottom line is non-positive.
There is a contingency fund for the conference series. Surplus from one year is used to cover deficit in another year, or to support other conference-related activities in the future years (say, sponsoring student travel).
There is a scientific organization (e.g. ACM) that runs the conference series and takes any surplus (and promises to help if something goes wrong).
The local university that organizes the event will keep any surplus (and they will also be responsible for helping if something goes wrong).
The local organizers will figure out some way to avoid surplus. More free coffee, additional student travel grants, last-minute conference fee discounts, additional awards, free city tour, honorariums for keynote speakers.
Some part of the income can be flexible. For example, the registration fee for local participants may be fixed only after the conference, once all other income and expenses are known, so that the bottom line will be close to zero if possible.