Amos Alonzo Stagg. Depending on the source, he compiled a record of 340-201-36 (Source: McClatchy Newspapers) or 314-199-35 (Source: Wikipedia), but either way it's far ahead of Hayden Fry's 178 losses in a total record of 232-178-10.
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Tricky question since there are all kinds of ways people try to distort the counting of wins and losses (div 1a vs others, etc). However, Amos Alonzo Stagg (Sr.) had 190 losses and no coach was recorded as having more since he started losing games back in 1892.