I don't think this is quite the correct place to ask technical questions like that. You're more likely to get answers on stackexchange, but you'd have first to give a bit more details about your problem, it's quite vague.
When you're accessing a Windows-produced NTFS file in Linux, there is no Windows, only a Linux-mounted filesystem which holds that file.
Similarly, when you're accessing a Linux-produced FAT32* file in Windows, there is no Linux, only a Windows-mounted filesystem which holds that file.
In other words, a file is merely a file, and contained in a filesystem. If you can mount and access the filesystem, you can do anything you want with that filesystem, even up to deleting files contained within it.
* Windows can only read Microsoft filesystems, so the Linux-produced filesystem has to be one that Windows knows about.
Are you asking why Linux doesn't enforce the file protection modes when a NTFS partition is mounted?
It does however it has to map the NT user accounts to users and for ease of use the mapping is to map all of them to a single user.
When an NTFS partition is mounted as a removable disk, the protection is ignored, and all files are readable and writable in the same way that a FAT partition would be. The ownership of the files is assigned to a specific user. Normally the one that requested the mount.
