Does the kernel print any messages when interrupting the boot process? I can't think of any config options of the kernel that cause such behaviour, but there are too many to be sure that there isn't one of that kind.
Applying -rt should work fine if you're doing the following:
$ cd /usr/src/linux
$ patch -p1 < /path/to/rt-patch
Replace "/usr/src/linux" with your kernel source dir if you did not link it to /usr/src/linux already and replace "/patch/to/rt-patch" with the path to the rt-patch.
I guess you just missed the "<" after the -p1 option for patch. This makes the shell read the given file and pass the output to the given command.