Prudence, indeed, will dictate that governments long established should not be changed for light and transient causes; and accordingly all experience hath shewn, that mankind are more disposed to suffer, while evils are sufferable, than to right themselves by abolishing the forms to which they are accustomed. but when a long train of abuses and usurpations, pursuing invariably the same object evinces a design to reduce them under absolute despotism, it is their right, it is their duty, to throw off such government, and to provide new guards for their future security.” the theme of this passage from the declaration of independence is best described as: experience shows suffering new governments provide security long-term governments should not be changed lightly discomfort can be endured, but abuse will not tolerated

Lightly discomfort can be endured but abuse will not be tolerated.

I mean he does say that "governments long established should not be changed" but only for "light and transient causes" which is saying the part that discomfort can be tolerated for the sake of the safety a government provides. 
Then he explains that humans tend to suffer abuse instead of doing anything about it. But it only reflects on experience and does not make claims about if governments should be kept or not. 
Then, Jefferson goes and explains the part about not tolerating abuse. he makes the distinction between light discomfort and abuse by characterizing the second as a "long train of abuse and usurpations pursuing invariably the same Object [which] evinces a design to reduce them under absolute Despotism." Then, in this case, argues Jefferson, "it is their duty" to overthrow the government.