I really like Lets's Encrypt and have used it for my personal servers for some time now.
Other than the significant task of renewing these certificates don't see any technical killer arguments against using the free certificates in many a small bus...
I agree, it is important to understand the inherent risk of sharing private keys across unrelated services or varying security classifications. A widely used key may indeed be a bad idea if site impersonations (or session replay if you lack PFS) are...