1. If you leave IT funding in the various agencies and departments, then they are constantly faced with decisions like: "do I fund the new system X that will update and modernize our IT systems or do I put 10,000 more kids on health insurance next year?"  The way our government works, the latter is likely the right choice. 
2. If you fund IT out of a separate pot of money, then everytime someone goes looking for money for their special interest (and everything is a special interest) then your pot likely takes a hit.  You can get a vote by taking money away from IT system X and giving it to the homeless, or the environment, or anything else, any day of the week.

Its easy to say that politicians need to have more backbone and stand up to this kind of thing, but having seen this process from the inside now, that's easier said than done (remember the old joke about sausage?).   Anyone can say "I'll stand up to the special interests and bring good management to government." but the reality is that this is built into the way out political process works and what the press (because of its readership) finds interesting.  I can get a rally at the capitol everyday about a lot of things: IT isn't one of them. 

Part of the problem is that mostly IT companies are very politically unaware compared to their cousins in other industries.  Very little lobbying goes on by IT companies.  This means that IT issues are likely to be seen as "unimportant" by the harried legislator who has lots of people vying for his attention.