True understanding in how to be a good uke takes a long time. You're practicing something where you know what's coming. As uke, you must remember that you're there to help nage learn the technique. So a one mindedness on the appropriate attack is important. If you give the wrong attack, then it's hurting instead of helping.
BUT , you must also learn to give appropriate responses. By seeing the atemi come 1,000s of times you generally get the hint that you're not gonna get popped in the face my most people. (this is a bad thing, in higher levels, you should absolutely get hit if you don't do something about the atemi) As uke you must keep an open mind. When you go to grab someone, you don't do it with the intention of rolling off nage's right/left side. Doing so makes it EXTREMELY hard to actually learn a technique correctly. You attack with the intention of attacking someone. How many times have I just stood there while a shomen uchi just went harmlessly by without even moving?
Aikidoka are often in the mindset of harmony. But good wouldnt exist without evil, and you must learn the offensive mindset to be a good uke and as nage to know when you're leaving yourself open.
Now, when you start aikido, uke must help nage learn how the energy flows, so there is a lot of help going on there. But as you get better the help goes away. However, many ukes like myself have a hard time understanding where a nage is on that path of progression, or how to really help nage with this aspect of Aikido. When I first started I was very gung-ho about attacks. "Always give a good strong attack" was my motto. Now it's more, "Always give an honest attack, pare your [power/speed/secondary attacks] by nage's experience and ability.
Being a good uke is hard.
[This disjointed thought brought to you by bcole23]