It was because of politics and economics in general, and Bill Clinton and his cabinet in particular. Even before the infamous "Bottom-Up Review" of 1993, Clinton and his new Secretary of Defense, Les Aspin, announced and began to implement major cuts in defense spending. While some cuts were warranted, most of the cuts effected under the Clinton/Aspin regime were driven far more by porkbarrel politics, bribery and cronyism than force strength assessments. And our military suffered accordingly.
Remember the "peace dividend"? That was a euphemism for castrating our intelligence and military capabilities, leaving us blind and weak (compared to the Reagan years). Certainly, our laxity toward national security during the 1990's has cost us dearly (not to mention the flat-out treasonous acts of Clinton and his henchmen), and we have a lot of catching up to do.
From Cost-Effectiveness of Conventionally and Nuclear-Powered Aircraft Carriers, GAO/NSIAD-98-1 -- August 1998. Note that the "Bottom-Up Review" started after March 27, when Clinton an Aspin announced massive defense spending cuts:
In fiscal year 1993, the Navy decided to decommission the newest class of nuclear-powered surface combatants instead of refueling them. These ships are being inactivated after an average of 17 years of service and with nearly half of their planned service life remaining. The decision was based on two factors--the need to reduce force structure in order to recapitalize the force and the ships' need for expensive nuclear refueling overhauls. Faced with declining budgets and large fiscal requirements, the Navy determined that the midlife modernization and upgrading through a refueling complex overhaul were not cost-effective.
They were mothballed because they were considered too expensive to maintain and operate. God help us if they get this tight with submarines!