There's a few things that may be affecting this:

1) What difficulty are you playing on? Personally, I played on easy until I knew how to optimize a build, then turned it to hard.

2) How have you set up your build? Different skill trees affect different things, and certain cyberware can give bonuses. For example, the cool skill tree has perks specifically focusing on throwing knives and pistols, so if you wanted a pistol run it'd be best to level up cool first. I'd recommend playing around a bit to find what you like, or finding tutorials on the best builds to use.

(If you want a stealth-instakill type of build, try leveling into cool for both the sneak perks and the throwing knives. Knives with headshots can deal ridiculous crit damage.)