It's politics, both internal to the BBC and nationally.
The biggest part of the BBC's funding comes from the license fee, which the government have frozen, and another chunk comes from government grants, which are also on a downturn. So, there's less money going into the BBC than a few years ago, and there may be more going in in future (or not).
Of course, in addition to how much money you have available there's also the question of how you spend it, and it looks like the current powers-that-be at BBC are less friendly to Doctor Who than their predecessors. And so the team get less money to make the show. A few years from now, once those powers get replaced with other ones, who knows?
(Incidentally, it's perhaps worth noting that the situation in 1989, when it was cancelled, was similar: the BBC budget was under pressure from the government, and also the internal regime was less-than-friendly towards the show.)