He says this because, as the story later turns out, they regret those plans and it all turns out just the opposite of how they intended.  He specifically states, "It was, as Bill afterward expressed it, 'during a moment of temporary mental apparition'; but we didn't find that out till later."  So, they had what they thought was a sudden light bulb of a great idea, but it doesn't end up being a very good idea at all.  Their charge is simply awful to be around, and Bill has to put up with all sorts of mischief and degradations at his hands before they finally decided to pay the kid's father to take him back.  Not a very successful kidnapping scheme at all.

It also helps to understand that O. Henry is a funny writer; he often has a sarcastic tone to his stories, and Bill is being funny and a bit sarcastic when he said this.  The entire story is very funny, and Bill's sarcasm throughout aids in that humor.  So knowing O. Henry's writing style, and the rather wry character of Bill help us to understand that the comment was made in sarcastic hindsight.

In "The Ransom of Red Chief," why does Bill regret the kidnapping plan?

Sam recalls Bill saying this because of how badly the kidnapping turned out. They made a bunch of assumptions which led them to believe it would be an easy scheme of a kidnapping and collecting a ransom. First, they assume that in a "semirural" town, family ties are strong. Therefore, the close-knit community will come together if a child were to be kidnapped. Also, being in a small town, Bill and Sam wouldn't have to worry too much about snooping press or a large police force. They happened to be right about this, but it is possible that Johnny's father didn't even notify the police. 

They assumed that it would be easy to dupe a simple man from a small town. They assumed that Ebenezer would come up with the ransom immediately upon hearing of his son's abduction. They didn't expect the kid to be so rambunctious nor did they expect that his father would be reluctant to pay the ransom. They certainly didn't expect that they wouldn't be able to handle, or even babysit, Johnny. In short, they made a number of assumptions that turned out to be wrong. 

Bill, in particular, says that they were not thinking clearly because he was the victim of Johnny's relentless and sometimes violent games. Johnny leaves Sam alone for the most part, but he terrorizes Bill. So, of course, in hindsight, Bill tells Sam that they were in a "moment of temporary apparition" to emphasize how badly it had gone. Bill also says this to insist that they should never try such a thing again.