From my dealings with DIO and DE in a previous incarnation, my view is that they are stuck in the unfortunate position of being perceived as 'nasty people' despite often having hugely passionate people working for them.
The problem is twofold - firstly it is the issue that DIO has to be seen to either put the buildings to defence use (i.e. part of the MOD) or show how it is diversting itself of them, either to Govt or private sector. This means having to be absolute b@stards, and insisting on charging for things used by non MOD assets, because HMT has to see things done properly.
This is because in the good old days it was possible to turn a blind eye, but nowadays the media (self annointed guardians of moral justice) would hit the roof if they saw public buildings being used in a manner outside that laid down by the rules - no matter how worthy the cause is.
From DIO perspective, if they make an exception for one, then they are going to have to make an exception for all - would you like to see a charity supporting hugely dubious causes insisting on its right to free access to MOD facilities including power, maintenance and the like, because the real fear is that a cause we like gets a break, then plenty of others we may be less supportive of may get a good claim on these sort of facilities too.
There is the wider issue though as well of the defence budget being used indirectly to support private enterprise or charity, which raises all manner of issues over the use of public funds innapropriately.
Let me be clear - I think the Nimrod charity is a great idea, I hope it does really well and when I'm up that way later this year I'd love to put some money in their pockets if they are open. BUT I equally feel that once a plane is struck off charge, or a ship off our books, then it is no longer the responsibility of the public to provide funding indirectly for private charities - no matter how worthy they may be. The budget is squeezed to breaking point, and I'd rather we spent every scarce penny on inservice people, and not those charities showing out of service kit. I also don't want precedents set which means charities or causes that I would have real issues with using lawyers to find loopholes or exploits enabling them to use our facilities for free.
Ultimately its not the people at DIO to blame (both civil and military)- talk to them and you'll see the passion for defence in what they do. Someon though has to implement rules, no matter how distasteful people think they may be - it doesnt mean that they dont give a damn though.