Since Spotify wields an enormous influence over what music becomes popular, labels can treat it as a loss leader and keep pumping money into it that they make back from album sales/tours/merch/etc on their top artists. The issue with this is that it vastly favors labels who can leverage this economy of scale, and independent labels for whom album sales are a larger slice of their income can't weather the decrease in payment as well.
This is further exacerbated by the fact that Spotify divides payment per stream up by the total number of streams. Simplified example: if I stream two songs in one month, an indie artist once and a major artist once, they'll each get $5 of my $10. If I stream the indie artist once but the major artist twice, however, they get $6.66 and the indie artist only gets $3.33, even though I the amount I listened to them didn't change. (edit, the pool is actually comprised of all users, I just used one in this example for simplicity)
All this adds up to a system that is heavily stacked in favor of major labels and their respective artists at the expense of independent ones.