To put it bluntly, it's because she has almost none of the tools that other Marksmen have.
She lacks range, and I'm not talking about her attack range, we all know it's the average 550. No, I'm talking about the fact that none of her abilities extend beyond that attack range. If she's using Tumble aggressively, the longest range she can pull off an attack is around 750-850 on a target running away from her (depending on their MS). A lot of Marksmen, and non-Marksmen for that matter, have abilities that can reach farther than that without also expending mobility.
Her base stats are average, and she has only one other steroid in her kit. And it's an AD steroid, so it doesn't affect her W proc rate.
Her CC is situational, and almost always only usable to either engage or disengage a fight. It's difficult to guarantee her E stun on a target moving in a fight, as it's not fire-and-forget CC.
Her mobility is built more for chasing targets than for escaping them. Her Tumble can get her a bit of distance if her pursuer is relying completely on movement speed, and her Condemn can stop one person from chasing her sometimes.
Like most Marksmen, she's exceedingly vulnerable to CC.
Silver Bolts even has some mechanics to make it super obvious that she only benefits from engaging and staying in fights. If she attacks another target, any previous target's stacks go away. If you can get in and out of fights faster than her, you kill the damage from Silver Bolts.
Finally, while Armor and Health do not stop the true damage from Silver Bolts, it makes the majority of her damage output take much longer to kill you. If Vayne was only dealing damage through Silver Bolts, she could guarantee a kill in 13 procs. Which requires 39 attacks. Even at the highest attack speed (which would make Tumble's attack reset slow her down, thus making it a waste outside of chasing/repositioning), that would take more than 15 seconds of constant attacking. But Vayne doesn't take 15 seconds to kill someone, she usually takes 3-5 seconds, because the other 80-90% of her damage output is 100% Physical.
The entire purpose of %HP True Damage, in the rare cases that it is implemented, is to have the same level of threat against tanks as she does against squishy champions. Marksmen in general are built to shred tanks, but Vayne is the queen in that regard. They built her kit around that ability.
Also, Vayne's not the only one. 