I disagree with the consensus. Incumbent presidents running for re-election tend to win, and the election of 1912 was in the middle of a strong Republican era. As it happens, Hoover's loss in 1932 was the only time since the Civil war that an incumbent president was defeated WITHOUT a strong third party candidate, data that goes somewhat against the conventional wisdom. Taft was not in as bad shape in 1912 as Hoover would be.
(1) There was nothing unusual in incumbent presidents--including some more popular than Taft--losing their bids for re-election. Cleveland lost in 1888 (granted, "only" in the Electoral College). Harrison lost in 1892. (Harrison's loss in 1892 can be blamed on the Populists only if you assume the Weaver voters would have overwhelmingly backed Harrison. This is very dubious; Weaver voters were dissatisfied with the status quo and had certainly contributed to the Democratic landslide of 1890.
https://en.wikipedia.org/wiki/1890_United_States_House_of_Representatives_elections) There are also presidents who might well have lost if they had been nominated for a second term, such as Arthur in 1884. In fact, after Lincoln, every president except Grant who sought a second consecutive term was defeated (either for nomination or in the general election) until McKinley.
(2) 1912 was not "in the middle of a strong Republican era." It was between two strong Republican eras: that of 1894 to 1910 and that of 1918 to 1930. There were already signs of the waning of Republican domination in 1908, disguised by Bryan's defeat (the Democrats gaining five seats in the House on top of the 32 they had gained in 1906; the election of Judson Harmon as governor of Ohio and Thomas Marshall as governor of Indiana). 1910 definitely marked a turning point: the Democrats gained control of the House and won the governorships of New York, New Jersey, Connecticut, Maine, and Massachusetts. This was clearly a repudiation of Taft (although Republicans close to TR, like Henry Stimson, also lost), and there was no indication that things were getting better for Taft in 1911. Indeed, as
The Nation noted in its January 11, 1912 issue, much of the anti-Taft sentiment in the GOP was simply due to a feeling that Taft could not win:
"Taft 'cannot be elected.' This feeling is undoubtedly the true reason why many Republicans have faintly hoped that he would withdraw from the field. But as he has now definitely and even defiantly refused to withdraw, the real question before the party is: 'If Taft cannot be elected, can any Republican?' More specifically, the question is whether any Republican can be elected over Taft's dead body. It is confidently said that Roosevelt could be elected, but could he? Could he, that is, if he first had to go out and make open war upon Taft, with all the imputations of false friendship and desperate ambitions upon his head, with his party torn asunder in the process, and with countless Republican enemies eager to pay off old spites? Under those circumstances, it would not be a cool judgment that maintained he could win."
https://books.google.com/books?id=jWE5AQAAMAAJ&pg=PA27
Likewise William Allen White wrote in 1911 that "Wall Street sees that Taft cannot win. Wall Street fears Wilson. Big business will dump Taft mercilessly. It seems to fear that Taft's weakness means the success of La Follette..."
https://books.google.com/books?id=H3ZNAAAAYAAJ&pg=RA1-PA249
(3) One other point relates to the Debs vote (which you mentioned): one reason it was so large is that many voters thought it was "safe" to vote Socialist because the "reactionary" candidate Taft (not that Taft was really a reactionary but we are talking about perceptions here) had no chance of winning and the election was bound to be won by a "progressive" candidate, either Wilson or TR. If it was a two-way Wilson versus Taft race, many of them would vote for Wilson--as indeed they were to do in 1916.
In short, the idea that Taft could not win a two-way race was widespread at the time, and was very likely correct. You may be right that Taft was not as unpopular in 1911-12 as Hoover was in 1932 but you don't have to lose by eighteen points to be defeated. Big midterm defeats for the party in power, like those of 1890 and 1894, usually meant trouble for the party in the next presidential election, and there is no reason to think 1912 would be different, at least if Taft were the Republican candidate.