Wow! I use a Griffin FM transmitter and while I admit its not 100%, it's nothing like as bad as others experiences - one thing I did find was that it sounds worse when just running off the iPod - however I use a flexible arm plugged into the auxiliary power socket to power it up [2 hour commute each way exhausts the iPod Nano battery!] and the reception is noticeably [and I mean noticeably] better when it is in this configuration. My Eos is due 'any day now' [was delayed with this shipping backlog alluded to in various posts!] and I will compare the quality as I will have the direct hookup. Currently its running through a Bose upgrade Audio set up and I can have it as loud as I want without distortion. So problems 'may' be down to the power/transmitter/radio match and set up.
Having said all that, direct connection HAS to be the best way!! Hope this helps
Paul