Yeah, adding CAs to the store sucks. On Linux it needs to be in /etc/ssl/certs (this varies slighly per distribution), which is only writable by root. A single user can't trivially trust a CA, and a great deal of applications/libraries don't support overriding the store's path.
It's worse than that. OpenSSL uses /etc/ssl/certs (or sometimes a different directory, depending on the distro) by default. But Java uses its own store that uses an incompatible java-specific format, and Chromium derivatives and Firefox have their own trust stores. So to add a CA to a system it is often necessary to add it in multiple places.