Consider government, large corp, etc purchase requirements. "Oh SIP is the standard. Cisco do you support SIP?" Cisco says "Of course!". Check the box and buy.
Meanwhile at the time their ecosystem is 99% Skinny (their proprietary protocol) and SIP is an afterthought for anything other than extremely basic call functionality, trunking, etc. Even when pushed to release SIP firmware for their (at the time) $500 hardware phones the SIP firmware was so feature crippled you're literally throwing money away by using it.
So everyone installs Call Manager to be done with it and have something that actually works. Even when Cisco got around to essentially being SIP native getting 30 year old features like hold, transfer, busy lamp fields, provisioning, etc working between vendors was nearly impossible.
Repeat for just about every implementation in existence.