My dome light quit working in my 2004 Honda Civic along with the lights around the shifter. I checked all the fuses and none of them were bad. Now the lights around the shifter are working but my dome light is still not. What could be the problem?

Physically change the fuse. Just because it looks okay doesn't mean it's not blown. Also try changing the bulb in the dome light as well.

Remember, there's an under-dash and an under-hood fuse box. To properly test the fuse and circuit, you want to test "through the fuse," by using a test light or multimeter:

https://www.askmehelpdesk.com/cars-trucks/faq-how-troubleshoot-repair-maintain-hondas-46563-3.html#post252145

Begin by testing all fuses and then test for power in the bulb's socket. If you have power, the bulb is bad or there's a contact problem. Many of these bulbs get very hot and can cause problems, particularly if they are accidentally left on over night.

Not trying to be smart a@@ but could you have the switch on the dash for the dome light turn off by mistake