I would have kept any backpacks on the back seat with me, regardless of size.
It may be advisable to find a good & reputable company and stick with them, for example I used Mr Toom's service a few times and have never had any problems.
Use the same company every time, you get to know them, they get to know you and a certain amount of trust can be built up.
Mr Toom ain't the cheapest at 1,200 baht each way but reliable.
toom39@msn.com
(+66)01-4827148
(+66) 03-0178066
Have you contacted to the company responsible or the police ? May not get your IPod back but perhaps worth doing ?