That's interesting, I'd never heard of the bones of a relative being kept permanently in the family butsudan. My impression is that it was the ihai (an engraved tablet, a bit more elaborate than the rudimentary stone ds7469ls has asked about) that carried the essence of the people in those butsudan I've paid my respects at. Then again, these shrines are maintained in addition to family graves.
Since graves are becoming increasingly expensive and difficult to get - or get to - for city dwellers, perhaps there are lots of families keeping the remains rather than transferring them.