I work with GIMP, so many of the tutorials I link to will be about GIMP.
This tutorial from Aubrey Watts covers the bare bones of making a cover in GIMP, and goes over the very important concept of layers.
And here’s a giant honking passel of tutorials.
From Popular Soda, the basics.
From Skye Warren, three things to keep in mind when making your cover.
Note: Readable text is on both of these lists.