I'm new to R as well and faced the exact same problem. But then I looked at my data and noticed that it is being caused due to the fact that my csv file was using a comma separator (,) in all numeric columns (Ex: 1,233,444.56 instead of 1233444.56).
I removed the comma separator in my csv file and then reloaded into R. My data frame now recognises all columns as numbers.
I'm sure there's a way to handle this within the read.csv function itself.