It's important to understand that Papers/*.pdf is not a regular expression, it's a wildcard pattern that causes bash to perform filename expansion, or globbing.
$1 represents the first argument to your script, so your for loop is only ever iterating over that one argument.
Use $@ to represent all arguments:
for i in "$@"; do
doi "$i"
done
Additionally, it is important to understand that Papers/*.pdf is not a regular expression, it's filename expansion with globbing.