From TFA:

"Major U.S. airlines such as American operate between 6,000 and 7,000 flights every day, making available flight numbers a limited resource.

Additionally, not every number is available for standard passenger flights.

Typically:

    Flight numbers 1 through 2949 are assigned to mainline operations.
    Flight numbers 2950 through 6099 are commonly reserved for regional services.
    Flight numbers 9000 through 9999 are generally used for ferry or repositioning flights.

Airlines must also reserve thousands of additional numbers for codeshare agreements with partner carriers."