There are many reasons people legitimately resist or oppose having temporary protection orders made permanent. A temporary protection order is issued by a judge based on the statement of one side, before the other side has the chance to tell their version of the situation.
Having a protection order become permanent may impact rights to own or possess firearms. It is also possible that, in the days of the internet, the existence of a civil protection case may be easily discovered by a prospective employer and limit job opportunities.
A permanent protection order may be amended after two years but the procedure to do so is quite complicated and uncertain.
The two most obvious reasons to resist a protection order are (1) The events stated in the complaint simply are not true or (2) even if certain behavior did occur, it did not rise to the level of violence or threats required by law to constitute domestic violence.
There are other options on the first hearing after a temporary protection order is issued. Both sides may agree to continue it as a temporary order for some extended period of time. It is not uncommon, for example, for a temporary order to be issued at the start of a divorce case but to have the terms relaxed or the entire order ended at a later date.