Calcium for Humans: Supplements vs Fortified Sources
This is close to a personal medical question, so I'll try and be vague and avoid advice.

There's nothing inherently bad about calcium supplements, and those links and thousands of others that are easy to find tend to all say that same thing.  Basically, for typical people on a typical diet, enough calcium is supplied through food that supplements are unnecessary.  The problem arises when people take too many supplements, such that their intake is significantly higher than the daily recommended intake.  These people can experience a number of symptoms, including kidney and heart failure.  Fortified food and supplements are, as best as I can tell, no different, except that food is simpler route for intake with built-in limit-setting.  That is, you can easily pop five calcium pills (BAD IDEA) but nobody is ever going to drink five containers of fortified soy "milk" on a whim.

My go-to example is that of astronauts.  Astronauts who are in space for extended periods of time must take calcium supplements, in addition to a strict exercise regimen to help stem the tide of bone loss.  Bone loss still occurs, however, because they can only take so much calcium before it starts to cause serious heart problems.  There's nothing inherently wrong with calcium supplements but for most people they are completely unnecessary.  You should talk to your primary care physician and perhaps a dietician.