Sometimes in your Project Explorer you will see:
If you see a red exclamation point, then make sure to expand the folder and then click on src/main/java and it will turn blue. Then hold down ctrl and click on src/main/resources and then both will turn blue.
Then right click on one of the two highlight folders and hover over Build Path and select Remove from the Buildpath. A window will pop up saying it is removing the files from the path. Once it goes away the folder src will expand and inside of it the file main will expand. There will be java and resources highlighted inside of there.
Right click on java and then hover over build path and then select "Use as Source Folder". After you have done this the red exclamation point should go away. You can then run your mod and everything should appear just fine.
If after doing this the Red Exclamation point is still there, then reply to this article and say you are still having trouble. If the Exclamation point is gone, but you are still having trouble running minecraft then follow this link: