Ken wrote:

Why would they be? The last franchisee was named after the route, not
vice versa.

The last franchisee was not named after the route. The franchisee was GoVia
Group. The trading name that they used for their services was Thameslink,
which happened to be the same as the franchise name. The current franchisee
is First Group. The trading name that they use is First Capital Connect -
but the name of the franchise, as far as the DfT is concerned, is still
Thameslink.

Similarly, the Midland Main Line franchise is franchised to National Express
and operated using the trading name Midland Mainline and the Inter City East
Coast franchise is franchised to Great North Eastern Railway, who operate it
using their company name.

Not surprising that people get confused, is it?