Naming after a colour, or even a number, might make sense in certain other cities where major roads are not laid out in a grid and transit lines don't follow any particular corridor or street. But Toronto are has strong corridors, each with its own transit line, whether it be bus, streetcar, subway, and people recognize this, so I don't think there is any point of naming lines after colours. Naming transit lines after streets and destinations just makes more sense in the Toronto area.
The University Line doesn't follow any particular corridor, but it does serve all of University Ave, and it does serve University of Toronto and York University, so it is very easy for people to identify as the University Line, or the University portion of the Yonge-University Line. In Toronto, transit lines named after streets and destinations is more simpler than names after colours or numbers.