Oh yes, you can. My endometriosis doesn't magically make everyone else pain-free and illness-free. (If it did, I'd take it on the chin and celebrate; at least it would be for something.) Your flu is still awful. Your period cramps still suck. Your stubbed toe still hurts. My pain doesn't cancel yours out nor does it dwarf it.
I recognise the sincerity and generosity behind that thought: the recognition, even: and I appreciate it. The reverse can be horrific. A friend who's recently lost her husband was given some coping tips by a woman who said they'd really helped when she lost her dog. Sorry, what? You're comparing the loss of a pet to the loss of a husband? You don't do that. But it's not the other woman's grief that the friend objected to, just the comparison.
You can't compare pains. Sometimes people do, trying to find a place from which to relate to something they have no experience of. "Housebound? That must be really difficult, I spent a couple of days on the sofa with flu and it was so frustrating not being able to go out." That's well-intentioned and can be tactless (especially if they make a direct comparison). I try, in those cases, to respond to the intention, which is empathic. I can't expect people to know what endometriosis is like or to know what my experience of it is like, so if they're looking for an in to understanding, fair enough. If it's a very poor in, I can try and explain more, if they want.
But most people, in my experience, err in the other direction, so this is just to say - it doesn't matter how much pain I'm in, your pain still hurts too. And thank you.
(Apologies if the writing here is less articulate than I might wish. Sometimes the endo bit really does sabotage the writer bit.)