Minecraft already has a ton of sales, and is selling regularly for $27. If Minecraft were to join the bundle, it's profit would drop by a large amount, while it would likely not get a large relative increase in sales, since it's already incredibly popular. This most likely equates to a net loss.
On the other hand, many of these games didn't have many sales and sold for less, usually $5-$10 (going as low as $3). This means that when their price is reduced for the bundle, they're making a larger percent of their profit than minecraft would. For example the average price for humble is generally $0.75 per game (assuming 4 games and an average price of $4, with some to the humble company and charity), so something like Breath Of Death VII is still making 25% of it's profit per game, and selling a ton more games than it usually would. Even if it "only" sells four times what it normally would without the advertisement it'd still be as much as selling 1/4th of the copies normally... and let's face it, 150,000 purchases in a few days is way beyond what most indie games get normally, so games like Breath Of Death are likely seeing a large net gain (especially since it's digital and the sales use Steam's bandwidth). I mean at the average price, that's $112,000 in a few days. Small indie game makers certainly have a monetary reason to join.
On the other hand... minecraft would be making about 03% of it's profit... and is already selling tons (4 million total so far), the bundle wouldn't be nearly as large of an increase while also representing a large loss in profit per title given.
