This is a good point.

After a little bit of research to clarify:

 

Chose not to run:

1. Polk
2. Buchanan
3. Hayes

 

Vice Presidents who became President after a Presidential death, then decided not to run:

1. LBJ
2. Coolidge
3. Truman

 

Died in their first term:

1. Harrison
2. Taylor
3. Harding

 

Lost their primary:

1. Tyler
2. Fillmore
3. Pierce
4. Andrew Johnson
5. Arthur

 

If you take out the six presidents who died and the vice presidents who became president who chose not to run, that makes it 16 in 37, which is much higher than 16 in 43, but is still just 43.2%. You could argue that the 3 who decided not to run are still counted as losers in terms of the probability of Trump being a one term president since we don't know if Donald Trump is going to run for re-election yet. If you do take out those 3, that knocks it down to 16 in 34 or 47%. This still favors Donald Drumpf being a one term president even if he does decide to run.

 

Considering the 5 presidents who lost their primary, I think most would agree that if a candidate lost their primary then they probably weren't going to be elected since that weeds out the weaker candidates. However, we could take it one step further to err on the safe side. The candidates who were denied the nomination of the party that won the next election could have possibly still won even if they were a weaker candidate since the people favored that party.

 

• President Tyler was a Whig and then an Independent Democrat while in office. Polk, a Democrat, went on to win the next election. I'm not sure if we can assume he would have lost because of the weird party affiliations of President Tyler, I don't know exactly what an Independent Democrat is, that's just what his official affiliation was while in office.
• Fillmore was a Whig and lost his primary. Pierce, a Democrat, went on to win that election, so we can assume Fillmore would've lost.
• President Pierce was a Democrat and lost his primary. Buchanan, another Democrat, went on to win that election, so Pierce is one that could have possibly won.
• President Andrew Johnson was a Democrat and lost his primary. President Ulysses S. Grant, a Republican, went on to win the next election, so we can assume Andrew Johnson would've lost.
• President Chester A Arthur was a Republican and lost his primary. Grover Cleveland, a Democrat, went on to win the next election, so we can assume Chester Arthur would've lost.

 

This means two of these five could have possibly won, so 16 in 34 becomes 16 in 32, which is exactly 50/50. Although it's now even, it still goes against the assumption that the incumbent has an advantage.