Yea, it'll matter. With your FM radio it's ONLY receiving the RF signals, but with a wireless card it's receiving AND sending RF on the antenna. If it was just receiving then there really be any "danger" of frying the card, the only problem would be "bad reception" of the wifi signal....because each antenna is made to receive a certain frequency (or range of frequencies), the car antenna works best when receiving frequences from 87-107 MHz or so, but it's not going to be as sensitive to receiving 2.4 Ghz that 802.11g/b is on.
Get's a little trickier with sending because the when a radio transmits it's made to transmit on an antenna with a certain resistance/impedance, say 50 Ohms.... if the antenna is different from that then it's kind of analagous to hooking up your 4 Ohm stereo amp to a 1 Ohm sub or a 10 Ohm....things will get hot and not work as well, or you'll lose power and it still won't work as well. I think in one of the FAQs they cover this question.....I know I've seen a couple threads about this before.
I guess we learn something everyday because I had never known about the "pink foam situation" before these past few threads......will be carefull with new parts from on.