When you’re an end user you have no idea how the software that you use is made and nor should you. It is the job of the programmer to make the experience as seamless as possible and allow you to enjoy the experience without thinking about the insides. You can take a look at your operating system for example. If you use a Mac OS X type operating system then that means you just want things to work and you really do not care how it gets done. That means you are not going to be able to easily configure the operating system but you know everything else will just work.
If you are a person who uses the Windows operating system then you are probably the type of person who wants to be able to configure their system but do not want to get too deep into it. You want a custom user experience but you do not want to mess up the system at the same time. You may change the themes to the operating system and the back drop and maybe even go a little deeper than that. But when it comes to the internals of the operating system you tend to stay away from that. You also might be the type of person who would also want to change some of the hardware pieces of the machine. You might want to add more RAM or a bigger hard drive all while doing it on your own. Windows is built for that since the pieces of it are pretty much plug and play. It is not really hard to get third party hardware running on a Windows system.
If you are a Linux user then you are probably a person who likes to get really deep inside of their operating system. You not only want to be able to configure the cosmetic externals of the machine, but you also want to mess with the internals of the operating system as well. When it comes to Linux everything is configurable since the operating system is open source. Depending on how technical of a person you are then the sky is the limit on how much you can change the system. The operating system can be anything that you want it to be. There is no limit on what the software can run on. You can have Linux running on an embedded chip or on a gigantic super computer. It is really all about your mental and your financial resources.
Having a machine that is configured the way you like is a good thing to have. But you have to remember that the more configurable a machine is the more that you can run into problems. It is hard for programmers to secure all of the ways that the machine that they are coding for might be used. So they have to be careful but as always there is going to be some leeway given when it comes to convenience and safety.
But just because a machine is not as configurable as others does not make it necessarily more secure. That is what people thought about Mac OS X for a long time. Because of the low reports of malware people thought it was because something that Apple was doing. In fact it was because malware authors did not target the platform. And now that it is becoming more popular, we are starting to see that there are a lot of holes to be found on the system. Remember, OS X is able to be configured to a degree because you are able to install software on it.
When you have any system that allows the user to change any aspects of it there are bound to be holes. It is up to you as the end user to make sure that the changes that you are making does not lead to security problems down the line.