Check your SSL settings. The way SSL works in Neo4j is that you create an SSL "policy" and then you associate it with the various connectors (bolt, https, etc)
It sounds as though you got your HTTPS SSL set up, but maybe you haven't wired that SSL policy to your bolt connector.
In particular, the missing piece may be:
dbms.ssl.policy.bolt.enabled=true
OR
dbms.ssl.policy.<scope>.<setting-suffix>