I got it working now. It seems that the COLLADA format and its converters have lots of incompatibilites, versions seem to be very important. Here is a recipe to import MATLAB interactive 3D objects into Apple iBooks Authors to be used on an iPad.
1) Create a 3D object with MATLAB e.g. with SUFR and export it as VRML file using vrml(gcf,'filename.wrl'). 2) Import the VRML file into the free software MeshLab, switch off the light, export it as U3D file with colors and normals. 3) Import the U3D file into the free software Blender, remove the vertices of the cube, save as COLLADA DAE file. This file won't work with Apple iBooks Author. 4) Import the DAE file into the free software Google SketchUp and save it again as a DAE file. Maybe some of the problems of the DAE file of Blender are fixed by this. 5) Import the DAE file into Apple iBooks Authors.