I published wide using Draft2Digital, but refrained from putting my short Crux Skullcrusher and the Definitely Evil Sword on Amazon because of the $0.99 minimum, thinking it'd be pointless to have my work available free in every other market, but a dollar on Amazon.
But, after thinking about it, I saw no downside to listing on Amazon - basically I'd let the consumer make the choice. I listed on Amazon, and weirdly some folks started purchasing my short even though it was available for free on my website and other channels.
After a while, Amazon price matched my short such that it's now free for download, and since then, my visibility on Amazon has really picked up. I've been in the top 20 free short sci-fi and fantasy reads for the last week.
I say as long as putting your work on Amazon isn't keeping you from putting it up elsewhere, there's no downside thus far - especially for anything you're trying to release as a freebie.