I think the reason is that actually it wasn't meant to be germany-wide. The initial idea was 9€ per public transport network, but they quickly figured out that this will lead to many problems, as some areas have huge networks, others have many small networks and this would be one really complicated. But by then the 9€ message was out of the box and making it Germany-wide on a single ticket was the only way forward.
Consequence of late night negotiations on top level of the federal government, without involving respective experts from states, who are running public transport. ("Wait, we're subsidizing fuel, so we should subsidize public transport as well! Any quick idea?")
They are planning to reduce energy taxes on fuel for June though August, after they imposed CO2 taxes starting in 2021.
The German government tried to force people to use more renewable energies and electric cars by introducing the CO2 tax.
Since both are not adequate replacements, costs for heating, electricity and transportation exploded.
When the German government realized that was a problematic development and could push people into poverty, they hastily came up with the 9 Euro ticket and the fuel rebate (which is just reducing the energy taxes to a minimum) in the hope that the problems would resolve themselves alone sometime in the future.
However, the problems will be back in September when the rebate period is over.
Consequence of late night negotiations on top level of the federal government, without involving respective experts from states, who are running public transport. ("Wait, we're subsidizing fuel, so we should subsidize public transport as well! Any quick idea?")