Many Cisco protocols are proprietary simply because Cisco created a protocol to facilitate something where there wasn't an industry standard. For instance, Cisco created HSRP, and, eventually, submitted it for RFC approval. The industry feared extending the influence that Cisco has over networking, and it created a competing protocol, VRRP, which really does the same thing that HSRP does.
Cisco didn't change the Spanning Tree Protocol, but they extended it so that each VLAN can have a separate Spanning Tree instance (PVST: per-VLAN spanning tree). The industry created Multiple-instance Spanning Tree, but MSTP doesn't go as far as Cisco's PVST does. As rapid spanning tree became a standard, Cisco extended PVST to use Rapid Spanning Tree on a per VLAN basis (Rapid PVST).