You should kick it through the end zone every time if you can, in my opinion. What you are gaining by trying to tackle them short is far outweighed by the chance you give up a game-changing play.
Against UTEP, we kicked to them six times. The first kickoff was out of bounds. I'm not sure if we were trying to be cute and pin them in the corner but it cost us 10 yards (compared to a touchback). We got three touchbacks. On the other two, they returned it to the 16 (thanks to a weird pause by their KR after he caught it) and the 21. So we netted three yards gained on three kickoffs by not getting touchbacks.
Against Colorado, we kicked to them five times. We got one touchback. They also fair-caught one at the 29. On the three they returned, they got it to the 21 (after fumbling the catch), our 37 and the 25. So we cost ourselves 38 yards total by not getting touchbacks, including being a hare away from one being returned for a TD.
That's a pretty poor risk-reward gamble, in my opinion.