Experiencing PTSD, yes. Realizing that there are forces out there whose power levels vastly outclass Iron Man's, yes. Thinking they're all gunning for him? No.
There've been exactly 2 and a half direct threats to Tony Stark in the MCU: Raza/Stane, Whiplash, and Hammer. Pepper was only in immediate danger twice --- once during the Ironmonger fight, and then at Monte Carlo when she and Happy busted in on the damn GP and nearly got themselves killed by both Whiplash and a buttload of race cars.
Yes, actually, they
are gunning for him.
Stane had a gattling gun pointed at Pepper's face, Stark swooped in and tackled him away.
Vanko's drone was lying beside Pepper about to explode when Stark swooped, grabbed her and flew away.
Had Stark been just 2 seconds late either time Pepper would be pretty soundly splattered across the ground. This isn't lost on him, that thought would of course haunt him along with knowing it'll will likely happen again (you can stow the "it's only happened twice" non-argument, it doesn't have to happen dozens of times before he takes action. Once is enough.)
Loki and the Chitauri weren't after Iron Man. Hell, he wasn't even invited to the Avenger party by Fury; he invited *himself* and took it upon himself to start slugging gods and aliens.
"Weren't" and "wasn't" don't matter, they're past tense. Stark has since made a direct enemy out of Loki, and he probably knows Loki had powerful benefactors, benefactors that he'd be stupid to assume are perfectly fine with having their army destroyed.
His eyes have been (or are being) opened to the fact that there are beings out there much more powerful than he is, some of them he has directly pissed off. He knows he needs a safeguard for Pepper because he might not be so quick to the save next time.
*None* of that indicates that a sea of enemies is descending upon Tony Stark and poor Pepper. In fact, the IM3 trailers give every indication that the helicopter assault on Malibu is a complete surprise attack,
Do you realise how completely opposite those sentences are?
"there's no sea of enemies descending on them.... except for that incomming armada of helicopters sent to level their house with them inside it"
But that doesn't count because it's a
surprise attack, because all the other threats he's faced have sent him hand written letters, months in advance, introducing themselves and announcing the time, date and method of how they'll try to kill him. Anything else would just be rude.
Pepper is only a damsel if all she does is need to be rescued and doesn't have any other qualities. But she is infact an intelligent, highly capable, pro-active, CEO of a huge company. She also quite obviously can't stand violence, which is why if Stark make her an armour (which would be entirely logical) she wouldn't become a superhero, if the $#!+ hit the fan she'd get out of danger and try to think of a different way to help.
