I've tried the following:

$ avconv -i in.mov -codec:video copy -codec:audio copy -filter transpose=clock out.mov

avconv version 0.8.6-6:0.8.6-1ubuntu2, Copyright (c) 2000-2013 the Libav developers

  built on Mar 30 2013 22:23:21 with gcc 4.7.2

Input #0, mov,mp4,m4a,3gp,3g2,mj2, from 'in.mov':

  Metadata:

    major_brand     : qt  

    minor_version   : 537331968

    compatible_brands: qt  CAEP

    creation_time   : 2013-03-03 15:47:47

  Duration: 00:00:18.97, start: 0.000000, bitrate: 45882 kb/s

    Stream #0.0(eng): Video: h264 (Constrained Baseline), yuvj420p, 1920x1080, 44343 kb/s, 23.98 fps, 23.98 tbr, 24k tbn, 48k tbc

    Metadata:

      creation_time   : 2013-03-03 15:47:47

    Stream #0.1(eng): Audio: pcm_s16le, 48000 Hz, stereo, s16, 1536 kb/s

    Metadata:

      creation_time   : 2013-03-03 15:47:47

Output #0, mov, to 'out.mov':

  Metadata:

    major_brand     : qt  

    minor_version   : 537331968

    compatible_brands: qt  CAEP

    creation_time   : 2013-03-03 15:47:47

    encoder         : Lavf53.21.1

    Stream #0.0(eng): Video: avc1 / 0x31637661, yuvj420p, 1920x1080, q=2-31, 44343 kb/s, 24k tbn, 24k tbc

    Metadata:

      creation_time   : 2013-03-03 15:47:47

    Stream #0.1(eng): Audio: pcm_s16le, 48000 Hz, stereo, 1536 kb/s

    Metadata:

      creation_time   : 2013-03-03 15:47:47

Stream mapping:

  Stream #0:0 -> #0:0 (copy)

  Stream #0:1 -> #0:1 (copy)

Press ctrl-c to stop encoding

frame=  455 fps=379 q=-1.0 Lsize=  106291kB time=18.94 bitrate=45983.9kbits/s    

video:102724kB audio:3558kB global headers:0kB muxing overhead 0.008270%

The resulting out.mov plays just fine, but the video is not rotated. I've tried many different filters:

transpose=1

rotate=1

rotate=clock

All with the same result.