I have a 6 channel DTS file (44.1 kHz), using foobar2000 I converted it to WAV with the 5.1 to stereo DSP active so I can put them on a standard audio CD. Will there be any quality loss in doing this? As I haven't changed the sample rate and only downmixed the channels.

Theoretically, the downmix algorithm will result in the loss of some very quiet content from the surround channels, but, in practice you're very unlikely to notice any difference. Sufficiently unlikely that it's not even worth worrying about.

Thats good, it's only a CD for the car so it's not exactly a quiet listen environment and I'll obviously keep the DTS file as well. Just one other question is the sample rate of the DTS file really 44.1 kHz or is it just saying that because it's inside a WAV file?

I would suspect that it's really 48,000, but you should be able to identify that readily through foobar and do the resampling, if necessary.

It's a 1411kbps 44.1kHz DTS 6 Channel file, I guess some downsampling has already being applied to it.

DTS on CD has sampling rate of 44,100 S/s and actual bitrate of 1234 kBit/s.

For a more versatile downmix we can use the foo_dsp_downmix, the default output is the Dolby ProLogic II downmix to recover the original 5.1 when played in a receiver with dpl II decoder.

With a simple downmix, you can actually degrade the content quite a lot. There are many "spatial" effects that rely on signal phase modification across audio channels.
If you have a sound which is in two channels but has a negative phase in one of them, you may actually lose such sound entirely upon mixing.

For playback, I've been passing through AC3filter which seems to downmix quite well, should I just save the output of AC3filter?