Because, the apology issued was for "targeting" conservative groups. That was the apology issued. The IRS pegged blame on their own employees, referring to them as "low level workers" who didn't do anything politically motivated, but decided, on their own, to "target" conservative applications and subject these groups to additional screening, questioning, etc.
It makes no damn sense. Of course there was political motivation. Why else would you "target" these groups?
Because, if your "targeting" was SPECIFIC to the fact that you needed to undergo additional screening, reviewing, etc. because of the influx of applications - you didn't do anything wrong. You just did your job and the IRS should be defending you, not apologizing.