I have a fill valve that shoots water straight up every time the toilet flushes and I think I have a bad flapper as well. I'm comfortable with replacing the insides, seems pretty straight forward from what I've read. My question is, the water line to the toilet is basically a straight hard pipe, not the flexible tubing I see in the stores. While I'm replacing things, should I replace this or is this something I can't change out?

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shoots water straight up every time the toilet flushes

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Which type of fill valve do you have?

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water line to the toilet is basically a straight hard pipe

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Nothing wrong with that. The flexible lines are simply easier to work with.

If you have a correct angle valve installed I would suggest to replace the supply line too, also would suggest to buy a fluid master complete repair kit see the images below, Thanks.

John