More than 40% of the german railway network isn't electrified, which supports around around 10% of of traffic. Simply looking at
https://openrailwaymap.org/ shows you just how many small branch lines and less significant lines don't have overhead power for dozens of kilometers.
This means that for large parts of the network there is some traffic, but far from enough to justify electrification which costs around 1M€/km (and, with some tunnels, might even mean expanding the tunnel diameter). There is a reason DMUs are widely used for these lines, and expectations are that BEMUs might be even cheaper to run.
More lines should be electrified, but expecting it to cover everything is not realistic nor economically justifiable. See https://vm.baden-wuerttemberg.de/fileadmin/redaktion/m-mvi/i... for a study on how to run non-electrified lines in Baden-Württemberg which comes to result that BEMUs are cheaper for around half of the lines that full electrification.
I'm not aware of BEMUs getting some special subsidy (meanwhile electrification is heavily subsidised, IMHO for good reasons), looking from the perspective of the ones financing and specifying the operations.