According to Gordon Van Gelder, he's trying to do what he can within the budgetary realities of publishing. He's stated that, while he'd prefer to make F&SF available in as many formats as possible, the marketing and promotional opportunities available with the exclusive Amazon deal are too good to pass up.
http://www.sfsite.com/fsf/blog/forum/topic.php?id=833
I'm seriously considering making F&SF my only paper fiction sub, just because I like the mag so much and hate to give it up.