This is a very, very good point. Though, many of the functions that R provides just won't make any sense at all if you don't have an intuition for the statistics behind it. I have found myself reading the papers published about specific functions in order to understand the results.
Do you have any resources that you suggest for beginners in statistics looking to learn on their own?
Here's the resources I've used and found helpful (plus notes) for getting a least a basic grounding in statistics.
Khan Academy + "Head First Statistics"
-No matter what direction you want to go with your learning and before you start getting into street fights over Bayesian vs Frequentists philosophies, "stats 101" is the common base of 'statistics' for: Physicists, Engineers, Sociologists, Doctors, Economists, Journalists and more. Yes there are many "truths" in 'stats 101' that can be questioned, but this is the common language you'll want talking to any of these people.
"What is a p-value anyway?"
-A very quick, non-math heavy read on avoiding magical thinking in classical statistics.
"Data Analysis with Open Source Tools"
-I really love this book because it steps way out of "stats 101" land and gives a lot of really great real world advice and touches on many mathematical tools that can help you understand data. The chapter "What you really need to know about classical statistics" gives a refreshing overview of all the basic stats you've covered and explains many things that seem strange. Also the bibliography/recommended reading list from this book is fantastic.
The biggest thing I've noticed as I've learned more is that statistics is a gigantic field, and can mean extremely different things depending on what field you're in. Obviously learn the advanced statistics relevant to your interests, but when you get a chance listen to how other people think about stats, and keep learning.
I'm taking this right now. Can somebody provide some perspective on how thoroughly the course prepares you for using R? Does it give you a good enough grounding in statistics so that you won't shoot yourself in the foot with R?
Do you have any resources that you suggest for beginners in statistics looking to learn on their own?