Open the file in gimp.
Go to Layer>New Layer
Set it as transparent.
Ctrl+L
You will the the layers window pop up. This will be your friend if you ever start to do complex textures. Delete the bottom layer.
For the game, save as .tga without RLE compression. Or save as .png. Here's where I'm rusty, since I feel like Hampa's updated the site to accept .png and .jpg's but .tga would be best since I don't trust the site's converters.
Alternatively, you can go to Layer>Transparency>Add Alpha channel. You can now erase your art. Everything underneath will be the gray checkered pattern, that means it will be transparent.