No file has executable permissions when created unless you changed the default umask settings yourself. You always need to set executable permissions yourself.
What I want to do is, making all the files with a certain extension non-executable, So that Nautilus will prompt.
Nautilus has some options though (in preferences, behaviour, middle set of options):
What this does is check the file you click and check what the file is (by checking the shebang line or the 1st byte of the file) to see if it is an executable and offer to either execute, view or ask what to do with the file you clicked. Text files that have contain text (and not a shebang and/or code) will always open instead of getting executed.
Mind you: this is NOT based on extensions. Extensions are (/should be!) visual aids for us humans; not a way for programs to identify files (an MP3 named music.txt is still an MP3 and not a text file).