In a very basic form, yes, but it is also important to recognise that gender itself is a spectrum and there are non-bindary individuals (see also:
http://en.wikipedia.org/wiki/Genderqueer). Another user brought up a comparison before. Assuming you are a male, imagine everybody started calling you 'she' or responding to you as her. Imagine you were forced to use female or unisex bathrooms constantly, and comments regarding gender norms/stereotypes were applied to you as if you were female. Now, and this may be difficult, but imagine you had breasts, a vagina, and a body of a woman. In essence, your mind has been transplanted identically into a female body. Your, the cisgendered male that you are, mind has not changed in any form, and you are still absolutely certain that you are a male, you just have a vagina and breasts. You dress up as male, as you know you are, and people shun you, harass you, tell you you're disgusting and don't belong in the bathrooms/locker rooms you know you should use (in a society where gender neutral bathrooms are not a reality obviously, so male bathrooms for you). Every time you look at yourself, you know your body doesn't match who you are, every time says your name you know it should be a males, not a females. You try use certain facilities and people ask you about the state of your genitals, people comment that you don't look 'male enough' and an arbitrary line is drawn by some individuals suggesting that after this point (and huge amounts of money spent) you are 'male enough', and people are suspicious or make suggestions that you are faking or have some harmful ulterior motive. Suppose you know deep down that you are male and are in the wrong body but are unable to say anything as you may lose all of your friends, your family, be discriminated against, or be murdered, simply because of who you are, and are forced to hide and suppress this feeling that something quite seriously is 'up'.
For many, this scenario, although simplified (gender dysphoria can occur in a huge variety of ways, this is dissatisfaction and repulsion by one's own genitalia may be one form, and this also completely neglects non-binary individuals and intersex individuals), may serve as something which can be related to as a cisgendered individual.
I'm not sure if that serves as at least a starting point in understanding the experience of a non-cisgendered individual, because, it is important to emphasise, everybody's experience is different.