Fs1 ships have way better afterburner capacity than fs2 ships. Either way yeah, as soon as you let go of the afterburner, your ships decelerates. And doing afterburner pulses means that you'd need to turn on afterburners before your ship decelerates to whatever max engine speed you have it set at depending on what setting your engine energy at max will give you.
Also you have to wait for the burners to recharge. This can get you in a situation easily where you do a pulse, it recharges a little bit while your coasting and slowly decelerating to your engines normal speed. If you can do a pulse and have ample time to recharge while your ship is still decelerating to normal engine speed and pull off another pulse before you ship decelerates to normal speed. Then i'd say go ahead and pulse. But, since the afterburners can't really be cheated with, meaning their mostly inefficient enough to keep you from pulsing into infinity without dropping to your normal engine speed in between pulses and recharge enough to keep you from running out of engine energy.
This is also where i just find that i run away faster, and get to my destination faster setting the engine power at max and just lead foot, recharge all the way, and lead foot again. As opposed to the hard to do pulsing. Of course no one in this topic mentioned that they do use pulsing for afterburners into infinity without having to recharge from a total drain. Do people who pulse have this pulse into infinity in mind?
Also, don't forget, there's a limit to how frequently you can activate your burners. Meaning everyone who does pulse is forced to doing steady pulses, and not "hit the button as fast as you can" pulsing. That also affects burners big time. Otherwise i'd just set my afterburner button to turbo and have an above average cruising speed at any given time, especially with max engine power. The above average cruising speed wouldn't last forever, it'd still run out, but afterburners recharge reasonably fast. But all afterburners recharge slower than they are spent...another reason that factors into why i don't pulse, why it's faster for me to run away and get to destinations faster doing pedal to metal, recharge, repeat.
EDIT: Actually i just remembered it's different with all ships. Some ships recharge faster than they are spent. Some recharge slower than they are spent.