I used to have a problem with that. I can't remember what I did differently back then that caused it, but I don't have a problem any more with it. Normally I try to kill all horizontal velocity and tart dropping straight down at least 2500 meters up. Then I jut make sure that if the ground suddenly comes up that I have a low enough speed that I can decelerate quickly enough to avoid a sudden case of lithobraking, which usually mean below 100 m/s. My biggest problem is the ground not being flat, and my rocket landing, but since it takes an extra moment or two for one or two of the legs to touch down, the whole thing will start to tip over lowly. Most of the time taking off, getting up about 1000 meters or so, and then approaching again works. Putting extra fuel tanks around the lander and then putting legs on thoe helps a lot with the tipping problem, but sometimes rocket design doesn't permit that.
Right now my next objective is going to be getting up a chain of stations. I plan on getting one refueling and science station up over the Mun, Kerbin, and Minmus. Once that is done I can get a shuttle that can ferry science and Kerbals around, and hopefuly get an SSTO that can get to orbit and back to the space center. Chances are that it won't have enough fuel to dock at a station by itself, but i should be able to get a shuttle that can go to it and transfer supplies and kerbals to it. Doing so should ensure that I won't run out of money, as the only expenses involved after setting it up will be sending up refueling stations (Normally just the big orange tank with some solar panels and docking ports attached).
I tried playing with my flightstick, but I'm still more comfortable with my keyboard. Even with spaceplanes you don't need that fine of a level of control. The only really use I have for my Flight stick is mapping my stage activation button to the fire button, which has a cover that I can flip on and off.