I bought my large 2013 Giant Sedona DX, and my tender bits are extremely close to the top bar (I am 6') When I went in, based on stand-over I thought medium would be good, but I am glad the shop owner talked me into what I got. I have never cracked my testicles, and the bike is very comfortable for me to ride.

If you think about it, when you come to a stop, you rarely/never come down flat on both feet, and if you somehow slide off the saddle, a lower top tube only gives you an extra inch or two to gain speed before the crunching begins. And while mounting, I throw a leg around the back and put it on the pedal, so other than when I am standing over the bike during a short rest my jewels are quite a way from the bar. I think most of us are paranoid (based on memories of pain) but are pretty safe without any issues with a top tube that is close to us.