I'm of two minds on this one because I have a soft spot in my heart for the company, but I know that it is a Very Big Deal when Network Rail pulls a license.
I've done a bit of digging and the problem is much deeper than the one incident of a Driver passing a signal at danger (red). It appears that the management of the company had already been on very thin ice on safety grounds several months earlier and didn't take the actions to put things right; and the result? An extremely risky action, unfortunate for the Driver, and potentially catastrophic for many many more.
The company didn't have in place the safeguards to protect the public and - as far as I know - still hasn't. I've read three articles now on this, and i am sure that if the company can meet the requirements laid upon it by the deadline of the middle of this month - and has its licence restored - it will be watched liked a hawk by many and sundry.
It appears that the biggest failing was with management, and their training and records of same, and their understanding of the severity of what had happened, what was happening, and what would potentially happen.
Their entire license to operate freight and passenger service was lifted, not that of one engine.
I work in the same industry, and we are well aware of our responsibilities. We have all been trained in the what the deficiencies were, and we have been for many years. I'm proud to say that, as a whole, the UK railways are extremely safe. We safely move many millions of passengers every year with an extremely high safety record.