Part of the problem is that before SpaceX, the industry was used to "cost-plus pricing" in government contracts - i.e. "we'll pay you whatever it costs to make, plus some extra for you" - which strongly incentivizes the contractors to inflate the production costs (or, charitably assuming everyone is playing fair and 100% honest, there's still very little incentive to innovate in order to cut the costs down). ULA is still held down by that legacy.

Also, note that ULA is a joint venture between Lockheed Martin and Boeing; the underlying political issues form an infinite, money-sucking fractal. It's always been like that - space industry grew out from government military programs; in fact, SpaceX is representing the new wave of private, commercial interests with no military legacy.