First question yourself: are those penalties really unfair?...
It may appear that you simply forgot an essential thing or simply don't know some basic aviation rules and why they exist.

♦ Related aviation information: ♦

NTSB report of flight TW553 crash (25 fatalities, the origin of 250kts speed rule)
TWA Flight 841 Emergency landing (8 injuries - damaged slats due to excess speed)
NTSB full report of Spanair flight JK5022 crash (failed to set flaps at take-off 154 fatalities)
NTSB accident report of Crash ANC78FA074 (Failed to set proper light, 2 fatalities)
NSTB safety alert about loss of control (excessive bank angle, abrupt maneuvers etc)

Think twice and read or ask perhaps in the forum before disabling a penalty.


Penalties due to simulation limitation, or bug

For example: If you get an over-speed penalty, it's often because your weather add-on is not set properly and gives an instant (and unrealistic) burst of wind.
Another example is add-on airports that do not declare the surface properly which can lead to a "roll on grass & mud" penalty.

If you find a penalty really unfair or can't solve a bug you can disable them by editing the file: 'more_option.cfg' with Notepad.
Browse to your FsPassengers folder and open the file 'config/more_option.cfg' with Notepad.

Using this file you can disable for example:
'250kts speed below 10'000 ft penalty'
'disable the roll or landing outside landing strip penalty'
'disable gear speed penalty'
'disable flap speed penalty'
'disable overspeed penalty'
'disable G penalty'
'disable bank penalty'
'disable reverse thrust less than 60kts penalty'
'DisableDoorCheck'
'DisableFlapCheck'
'DisableTimeAccelerationCheck'
'DisableMaxPowerPenaltyWithBrake'

There are also other parameters that you can set, it's a really useful file.

Related questions:
How to find/open the FsPassengers folder
I got a penalty because FsPassengers said I made a dangerous landing/take-off?
I always have flap penalties?
I always have light penalties?
I have a penalty for exceeding MTOW?