Skyline has a feature in the Document Grid called the "Pivot Editor" which lets you group rows together based on the values in some columns and summarize the rest of the columns using operations such as Mean or Sum.

Here is the page with documentation about the Pivot Editor
https://skyline.ms/wiki/home/software/Skyline/page.view?name=PivotEditor

There is a document on there which describes how to calculate the CV of peak areas. I hope there is enough information in there so that it will be easy to see how to go about calculating the average peptide area across proteins and replicates.
If anything is not clear let me know and I will try to create a document that is more specific for your scenario.
-- Nick