As uke, you need to take care of yourself. As the uke, you are loaning your body to the nage, but - it doesn't mean you need to give your body up. As you progress through your aikido training, this may make a little more sense - allow the nage to use you, but don't give your self up to be injured.
Just how experienced was this nage? The nage should feel that the uke is not cooperating, and the nage should know if the non-cooperation is on purpose or if the uke just doesn't know ukemi yet.
If not, always let your nage know when you are not prepared to take a fall. As an instructor I will let a student know before hand whenever I am hurt or hurting. "Remember that my shoulder is hurt - so be careful on this side".
It is your responsibility to not get hurt. Take every precaution that is necesary - for your own good.
When I first started I had a terrible time learning to take ukemi. Luckily most of my nages were careful with me - but I always let them know at what stage I was at before we got into the technique.
I hope this helps.