When you got local people, "Home Guard" and other militia types doing partisan activities they tend to be honest folks fighting in the best way they know how, the Partisan Ranger Act could give them some protection from outright execution if captured, and I see nothing wrong with that or regiments of Partisan Rangers under military control and leadership doing their activities.
However there were too many bands of bushwhackers roaming the countryside from county to county, region to region who could not claim such noble reasons. A lot of whom were nothing but outright bandits who cloaked themselves in the guise of a "Partisan Ranger" serving the CSA to give them reasons to go wild. They outright abused it and preyed on people regardless of them being pro-Union or pro-Confederate. Arkansas and Missouri suffered terribly from those animals. Heck the one time Quantrill's Raiders were in Texas, there ended but being a running battle between Quantrill's band, the 5th Texas Partisan Rangers, with Bloody Bill helping the Texans!
Kind of hard to regard Quantrill and his men as true Confederate, or even true Partisan Rangers, when a Texas Partisan Ranger Regiment, (more like cavalry regiment though) were having running battles between each other.
Here's a good article on this stuff: