Just tested them all.
Low hit box characters:
Kung Lao - standing 1 combos, spin, 24
Reptile - standing 1 combos, standing 3, standing 2 acid ball, standing 2 invisibility, d4, dash
Cage - Standing 1 combos, b3, uppercut,
Mileena - standing 1 - standing 2 - standing 4 combos, d4, roll.
Sektor - uppercut, standing 1, 21 Teleport.
Sonya - standing 1 combos, d4 cartwheel
Jax - 123, 12-Overhead Smash, d4
Kabal - f4, d4 overhead, d4 dash cancel, standing 1, 11b3, enhanced dash, 21 Dash.
Quan chi - Uppercut, 11b2 Trance.
Skarlet - standing 1 combos, standing 4, d4
Non:
Scorpion
Lui kang
Sub zero
Sindel
Ermac
Kitana
Jade
Nightwolf
Cyrax - Thankfully
Noob Saibot
Smoke
Kano
Stryker
Shang
Baraka
Raiden
Cyber Sub Zero
Sheeva - Didn't even bother to test her.
Kenshi
Rain
According to the guy M2Dave, Jax is an S Teir character, which according to him, are characters with 2 bad match ups, but there are 10 characters that can punish him for using f4, and that list of 10 might not even include his two bad match ups that M2Dave listed.
NOTE: I have put in d4 for characters that have safe options after the D4, but all of these characters can gain d4 advantage on hit.