That's true; however, the entire focus of reconciliation is how it is used, not the fact that it is used in the first place. Budget bills are notoriously difficult beasts, and squabbles over the details are inevitable. Budget bills are also incredibly important, keeping the government running and adjusting what is spent to accommodate new circumstances.
When budget bills don't get passed — as in 1998, 2002, 2004, 2006 — Congress keeps spending money at the same rate it did the year before, which may or may not reflect current needs. Not passing a spending also violates the Congressional Budget Act, which requires that a budget be put into place each year.
It's important to keep in mind how difficult it is for the majority party in Congress to reconcile its differences with the minority when it comes to finances, given the differences between conservative and liberal opinions on the scope of government. But it's the pinnacle of partisan stubbornness and government waste when budget bills don't make it through.
Reconciliation allows budget bills to get past stubborn minorities. When the procedure was legislated in 1984, Sen. Robert Byrd, (D-W.Va.) put specifications around exactly which issues could be subject to it — all related to finances. Reconciliation can only be used for adjustments in spending, the debt limit, or taxes.
In this Congress, Senate Republicans are not budging on the issue of the Democratic health care plan. They're also holding their ground on climate change legislation. Since Democrats are two votes short of a supermajority in the Senate, Democrats must reach across the aisle to work with them — at least, for now.