Their contract with Starbucks is ending soon. Going forward their reader fees will be profitable to the company.
To swipe a debit card, Square has to pay at least $0.21 + 0.05% per transaction. 2.75% of any amount less than $7.75 doesn't cover the $0.21 fixed cost. They lose money.
Same deal with credit except it's $0.10+ (and 1-3.5%) instead, so they're only losing money on every swipe under $4.
There's also some amount of markup over interchange going to their underwriting banks (JP Morgan Chase and Wells Fargo) which makes the minimum charges at which there's any profit even a bit higher than that.
Basically, coffee shops are loss leaders for Square.