I'm not sure you understand your own questions.
To put something up in Apples' Appstore you must pay them 99$ flat, regardless of the software you use, even if a free one.
No way to run away from it, no way to avoid it.
Regarding "game makers", YOU must find the one you prefer AND hope it exports to IPad/IPhone, for which you'll REQUIRE a Mac, on top of a possible insane price for the exporter alone, if not using one of the services mentioned here.
C2 + Phonegap + Apple Dev account
Don't know, but will be a strain on your income.