First problem: matlab install requires libXp.so.6 library for xsetup and text-mode install does not work.
Solution: install xorg-x11-deprecated-libs rpm for fedora core from for instance rpmfind.net. This installs libXp.so.6 in /usr/X11R6/lib/libXp.so.6. In order for matlab to be able to find this library, add in directory /etc/ld.so.conf.d a file xorg-x11-deprecated-libs.conf with a single line containing /usr/X11R6/lib. Then run /sbin/ldconfig. After this the installation procedure itself did not report any more problems.
Second problem: When trying to run matlab, it does not want to start. Error message:
/usr/local/Matlab_R2006b/bin/glnx86/MATLAB: error while loading shared libraries: /usr/local/Matlab_R2006b/bin/glnx86/libmwlapack.so: cannot restore segment prot after reloc: Permission denied
Solution: I found the solution on comp.soft-sys.matlab:
chcon -t texrel_shlib_t /usr/local/matlab2006b/bin/glnx86/*.so
Alternative solution is disabling SELinux