"Pere" is French for "Father", and in this case the name honored Pere (Father) Jacques Marquette, an early French Jesuit missionary who explored the Midwest in the late 1600s and who died and was originally buried at or near Ludington, Mich. Ludington was originally named Pere Marquette, and the railroad's name was descended from a predecessor line called the Flint & Pere Marquette (i.e., Ludington) Railroad. (Ludington, of course, was the F&PM/PM/C&O's terminal for its Lake Michigan steamer and carferry services.)
All of which means that, Midwestern pronunciations notwithstanding, it's pronounced the French way -- PEAR, with accent over the first "e" (or "PAIR", if you want).