Of course, you might notice that still isn't enough to explain why Arcomage has around 1/1000000 as many active players as Hearthstone instead of around 1/10000 or even 1/1000, so here are three major reasons for the remaining discrepancy:
1. Advertising, recommendations, and addictive game design
work; Blizzard corporation was good at ensnaring customers well before WoW, and with it they honed their ability to the point it could be considered a health hazard. They made a game capable of consuming all of someone's free time even when that person hates the game, and then they have all sorts of incentives, both subtle and not, to make that person recommend it to all their friends, and that's after
the perpetual multi-million dollar international advertising campaign. People have to find
arcomage.net; they couldn't avoid finding WoW or Hearthstone without avoiding most of the game stores and sites in the world.
Of course, that also really isn't enough; corporations spend on advertising because they make a profit from it, but in the end you can't attract someone who isn't interested in the first place, which leads us to:
2. Arcomage is far from the only alternative to Hearthstone, and isn't even the first one people are going to think of; that advantage belongs to Magic: The Gathering. Which, notably, has two major methods of being played online; the official Magic Online service, and the open-source Cockatrice
software. After M:TG comes things like Yu-Gi-Oh, or even other strategic turn-based online games entirely.
Even then, you might think the distribution of players over these games should be more even, which leads us to:
3. Much like 3of0 said, the exact mechanics, interface, and attracted players of arcomage.net result in a very particular, narrow
pattern of timing, time taken, and games played— equivalently limiting those it appeals to. Players can't reliably (or conveniently, natch) co-ordinate to play games at the same time, or to predict when their next turn will come up when they can't. When players are online at the same time, they can't easily predict how long a particular game is going to last, or when the other player might be interrupted. The lack of popularity is both a draw to some of the players, and also self-sustaining by ensuring a player can never be sure any
other players are online when they want to play a game.
To summarize: popularity has a lot of things influencing it, most of them aren't fair or nice, and even accounting for all of them, this site appeals to a very thin slice of a very thin slice of the internet's population.
Edit: It only took two posts.