The goal of the congestion charge is not to make money off cars in London - it's an attempt to reduce the number of cars in London. The number of cabs is limited largely by the complexity of The Knowledge, while the number of minicabs is rather less limited, so in conspiracy theory land, TfL have motive to ban minicab operators wherever possible.
In any case, it's very unlikely that this is an ulterior motive - there's no reason why the problems aren't exactly what was listed, i.e. mostly administrative failures on Uber's part where other minicab companies are more cooperative with the license requirements.
In any case, it's very unlikely that this is an ulterior motive - there's no reason why the problems aren't exactly what was listed, i.e. mostly administrative failures on Uber's part where other minicab companies are more cooperative with the license requirements.