There are plenty of reasons to pay for a certificate. Wildcard certificates only came out last month on LE, and people might still be weary to switch their primary site over so quickly. Additionally, there's still a few cases I can think of where a custom certificate might be needed.

For instance, I recently consolidated my personal projects and site onto one server. I needed a single certificate that'd cover two domains. Digicert combined two of my orders into one certificate with two wildcard SANs. You wouldn't be able to do that with LE.

Edit: I was under the impression you couldn't do multiple wildcard SANs in LE but according to some forum posts it's fully possible as long as validation passes.