If an employee is marked as exempt from FIT, it will not be included on line 2 of the 941 as line 2 is "Wages Subject to FIT".
Line 1 of the W2 form is also "Wages Subject to FIT".
Some more clarification is that box 2 of the 941 is to show the wages reported in box 1 of the W2. And the W2 instructions are for "Total Taxable Wages", see from the W2 Instructions:
"Box 1—Wages, tips, other compensation. Show the total taxable wages, tips, and other compensation that you paid to your employee during the year."
Paul Mayer
ZPAY Payroll Systems, Inc.