Let's say that I want to study naive T cells so I isolate them from lymph nodes, for example, isolate by MACS negative isolation. Then plate them on 96 well-plates pre-coated with CD3 and CD28.
Because they are looking at T cell function. I'm not sure how else you can look at T cell function without stimulation/activating them. And you want to have them all activated in a certain way so that they are uniform in order for you to have enough population to study.
Naive T cells... the definition is just T cells that haven't previously seen antigen. So, yes, they are technically un-stimulated. To evaluate their function, the stimulation would simulate their first encounter of antigen.
I didn't read the paper, so I'm not sure what they did. But, usually, there is no "resting" since the CD3/CD28 can be considered as the first recognition of the antigen. Because CD3/CD28 will stimulate proliferation. However, you can also considered the CD3/CD28 as non-specific, and a rest and use of a specific antigen for restimulation...
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