@PinoBatch HostGator also charges a similar fee, and it’s very annoying.
If you’re looking for an e-commerce provider that does support Let’s Encrypt, Shopify is probably the most popular one. I’ll add it to the list.
EDIT: in the interest of being fair, I reviewed SitePoint’s top 10 list of ecommerce providers for others that might support Let’s Encrypt. In addition to Shopify, both Wix and Squarespace integrate with Let’s Encrypt and were already listed. Additionally, BigCommerce offers free SSL certificates, but they are supplied by Symantec’s Encryption Everywhere program.