It's rather naive to think that newspapers ought to be neutral (or fair) in everything they produce. What kinds of neutral is desirable? There's neutral tone or neutral political bias -- there are many different ways for a newspaper to be or not be neutral.

Assuming neutrality isn't something that we should expect newspapers to value, then I think transparency is an good alternative. A presidential endorsement can be a good thing in that the newspaper staff are being openly transparent about their political bias.