They look at the federal withholding tables, and withhold taxes per the table.

The table is inherently based on a projection of income. For most normal salaried jobs, people have a fixed income... little to no variance from paycheck, so the tables are based around that. If you take some unpaid leave and have a $300 paycheck and then the next month pick up over time and get a bonus/profit sharing, etc, and have a $6000 paycheck you will notice the percentage withheld is vastly different. A huge bonus will be overwithheld because they will withhold based on the table that would be commensurate with a much higher income than what you are actually making. Small variances work themselves out, but large bonuses are so over-withheld that they will yield a refund when you file taxes at the end of the year.