The difference is based on the source of the money used to pay students.
Work study is a federal financial aid program, and requires students to complete the Free Application for Federal Student Aid (FAFSA). When departments have a work study position available, they are only responsible to fund 25 percent of the wages, the other 75 percent is funded by the federal government. Each work study position has a limit to how much money can be used by the student. That limit is usually $2,000 for one academic year or $1,000 per semester. If the student exceeds the $2,000 limit a department will have to begin funding the entire amount of wages paid.
Hourly employment wages are paid entirely by a department through its regular budget. As you can imagine, if possible, departments like to use work study funds to subsidize the wages of their student employees. Students that are work study eligible have an advantage in finding campus employment because departments want to use federal funds when possible.