Wait -- is this for free or are they paying you? If they're paying you, but perhaps at a lesser rate than in their mag, is it a reasonable rate, given whatever other perks you might be getting (e.g., being able to use it as a reference)?
How prestigious is the mag/site? I can see, for example, being willing to take a nominal fee from something like GeekDad, because a) it gets a lot of website views, and b) it is reasonably well known, so it would make a decent reference for future work, and c) it might even lead to future work with that site and ultimately the magzine. Or perhaps something like the Alfred Hitchcock or Ellery Queen franchises(assuming they do something like this, which I don't know), because, again, they're so well known. OTOH, if it's a mag/site no one has ever heard of, there's not much up side to it.
Also, consider whether the magazine/site is in a niche area that is also your specialty, or a specialty you're looking to pursue. For instance, if you wrote about antique roses, and the mag/site was THE go-to resource for antique rose lovers, and you're planning to specialize in all sorts of gardening stuff (probably broader than just antique roses), where the readers would recognize that where you published was a top-notch place, even if they grow asparagus instead of roses, then that might be worthwhile. OTOH, if it's just a one-off article, not part of some grander career specialization, that would suggest the limited value of the sale.
And finally, consider whether there is another market for this piece. I've written some stuff specifically for calls-for-subs (by well-known mags/publishers), and if I hadn't made the cut for the magazine, but they'd offered me, say, a half fee for posting on the website, I'd probably have taken it. It clearly wasn't a scam, seeking free/cheap content, because they did run the stories they'd sent out the call for, and I didn't have any other markets for the story without spending more time rewriting it than I did writing it in the first place, so some cash would have been better than none.