Teams are allowed to pay players the league-minimum salary for their first three years in the majors. Not everyone does so, but there are teams who take advantage of this while they have the chance in order to help keep costs down both in the present and in the future -- it's likely that much easier for a player to argue their case in arbitration when the team has already gone out of their way to give them a raise in the past.
Sometimes, paying the minimum doesn't bother players. Mike Trout got the minimum from the Angels -- Mike Trout -- but then signed a six-year, $144.5 million extension during those years anyway. Sometimes, it does bother them: Gerrit Cole is currently grumbling about the Pirates paying him just $541,000, which is his 2015 salary plus a $10,000 bonus for making the All-Star team. Given Cole threw 208 innings with a 2.60 ERA last summer, you can understand his annoyance.
The Sox decided not to incur potential animosity when it came to their player with two years in the league already, and gave Xander Bogaerts significantly more than the minimum salary. Bogaerts will be paid $650,500 in 2016, which might not sound like much in the grand scheme of baseball salaries, but it's 30 percent more than what they could have paid him under the rules of the collective bargaining agreement. A 30 percent bump in pay for the work he's already put in is no small thing, especially when no one made Boston do it.
Now, we don't need to pat them on the backs for being philanthropists or anything like that -- the Sox likely gave Bogaerts a bump now to foster good relations later on, which they will likely need given Scott Boras is his agent. Trying to butter him up is likely better than annoying him, though, and Boras has no problem working on extensions before free agency so long as he believes that the team is fairly representing his client's value. In short, this can't hurt Boston's chances of keeping Bogaerts around.
He'll be arbitration-eligible for the first time in 2017, and his salary is sure to go up at that time. Then again, by the time Bogaerts is arbitration-eligible, the new collective bargaining agreement will be in place, and maybe the two sides will get to work talking extension instead of going year by year. It's too soon to know for sure, but at least we know the Sox didn't annoy their young, budding star when they had the opportunity, and instead decided on being comparatively generous.