In their S-1, SendGrid disclosed that it earned about 73% gross margins, spending roughly $18M in cost-of-goods-sold to earn $52M in revenue (six months ending June 30, 2017). Around that time, we estimate that they were sending roughly 30 billion messages a month, suggesting that they were spending $18M to send 30 billion messages - that's about $0.60 for every thousand messages.
If SendGrid's costs are universal in the industry, then that 10,000-message free tier, therefore, is costing Mailgun perhaps as much as $0.60 x 10 = $6.00 a month. If you have thousands of free accounts, the cost adds up rapidly on the P&L statement. I could be off by an order of magnitude about the sending cost, but you get the point.