I had the same problem and was also able to run yum install on suphp, but I ran into problems after that. The problems were blank webpages from testing webmail, phpmyadmin and the initial page for ISPConfig.
This was on CentOS 5.3 x86_64. Turns out this error was because I only had the i386 install of apr-devel (I think configure was looking for an x86_64 header file that didn't exist from the i386 install). Running "yum install apr-devel" got the x86_64 version, and then I was able to successfully use ./configure, make and make install on suphp after that.
Note, since I had already run yum install suphp, I had to delete the yum installed version of /etc/httpd/conf.d/suphp.conf and create a new one with only the line from the tutorial ("LoadModule suphp_modules modules/mod_suphp.so").
BTW, the newest version of ISPConfig (188.8.131.52) seems to work on CentOS 5.3 if you follow the CentOS 5.2 instructions. (and replace i386 with x86_64 if you use 64 bit).
Hope this helps anyone else who runs into the same problem.
Thanks for the great tutorials!