The AP article writes that "Messi received 41.60 percent of the points in votes by national team coaches and captains plus selected media. Ronaldo got 23.68 percent and Iniesta 10.91 percent." That makes it sound like Messi only had the support of 40% of voters in what was a straight plurality election. If that were the case, it would make for a very poor voting system, as it would allow for winners that only had the support of a small minority of overall voters.
Fortunately, FIFA does not use a simple plurality system. They instead use a weighted Borda Count, where all voters vote for their first, second, and third choices for the male and female players and coaches of the year. First choices get 5 points, second choices 3 points, and third choices one point.
Messi received 41.6% of the overall points--which is actually very high, because it is impossible for him to get more than 5 out of the 9 points that each voter was capable of awarding (assuming they listed three players). As ESPN notes, Messi did, in fact, receive a majority of first place votes from all three types of voters: team captains, journalists, and coaches.
Many sports use a version of the Borda Count in voting for the best player of that sport's season. Baseball's MVP awards use a system in which voters can vote for 10 players, with their first choice getting 14 points, second choice 9, third choice 8, and so on. In this year's American League voting, triple crown winner Miguel Cabrera soundly defeated Mike Trout with 22 of 28 first place votes, but just 362 of the 1652 total points awarded (22%). College football's Heisman Trophy is also awarded by Borda Count, with a first place vote getting three points, second place getting two points, and third place getting one point. 2012 Heisman winner Johnny Manzel similarly won a majority of first place votes but a plurality of overall "points."
Of course, it's possible to win a Borda Count vote without getting the most first place votes. That result would mean that the victorious player had a broad base of support among many voters, rather than just the ardent support of a few.
Either way, when a Borda Count system is used, the percentage of total points is essentially meaningless without full data of how many first, second, and third place votes each player received. News coverage of Borda Count results should accurately portray how the election was conducted--as they usually do in MVP and Heisman voting.