Is being featured on the front cover of a scientific journal an academic milestone? I am a PhD candidate now writing my thesis. 

I have recently submitted an article to a very good journal (for a particular yearly issue). Along with the article, authors were encouraged to send "cover images" for the issue. I enjoy drawing and illustrating, so I did. First the paper got accepted (with minor revisions) and a couple of weeks later I got an email from the editorial board saying my image was selected as the cover image of the issue. 

I got really excited at first, but a couple of questions come to mind now:


Since authors are encouraged to send their cover images, is the selection based on paper quality or just image quality/beauty? I'm OK with being recognized as a scientist that can draw (ish), but I'd rather be a good scientist whose work "made it to the cover". 
Does it have any academic value to be on the cover of an issue? Aside from being featured in the issue (which should generate a broader impact based on bigger exposure?), is it valuable/acceptable to add a line to my CV?
Yes, it is a plus, and yes, you can add it to your CV. But it is (and should be) just one thing among many. It, alone, won't get you a job or a promotion, but it adds to the list of things that are positive about your contributions. The academic value will be positive, but small. 

The paper is more important, of course. The image might induce a few more people to read your paper; a good thing. 

Congratulations. 

But your sense that you want to be known for the quality of your papers is the right attitude.