Being root is much different to being Administrator in Windows. As root, in linux, you CAN format your hard-drive, delete stuff like the init scripts, the window manager etc, requireing days of frustration and LOTS of coffee.... It's VERY dangerous to be root on a regular basis! In Windows, most programs won't work, or work crippled if you're NOT admin. An admin in win cannot do extensive system damage. In Linux, this is the opposite, as some programs will refuse to start if you're root (consider xQln - a math function drawer). A normal user in linux is able to install programs (not system-wide, but for himself), can run ALL programs, can change his own settings, can compile programs etc, can start/stop daemons (system services that is).. Plus, while in user mode, access to your kernel is restricted. In super user mode, it is not. Root is for system maintanence (janitorial) tasks ONLY and configuration such as network config and the such! I generally use it twice a day tops, for a few minutes. As standard user you have all FULL access to the system (more or less standard user in ubuntu is the equivalent of Admin in windows while an especially crippled user, given access to almost no groups in ubuntu is equivalent to user in windowz).
Synaptic DOES NOT INSTALL WITH YOU AS ROOT! It installs on a user account with you having root priviledge. It asks for YOUR password, not root's (as does, let's say Mandrake's package manager), so you being true root won't help.
Ubuntu doesn't employ standard root procedures, as it doesn't have a root account enabled. You'll need to create it. In order to create it (it's useful, as you can use su, a simpler command than sudo) type this at the console
Then, you will be asked to provide root's password. DO NOT LOG ON AS ROOT. Use SU! And if you are using Apache, you should give yourself rights to the folder rather than using root!