Perseng for many it simply comes down to whether you wish to...

Perseng for many it simply comes down to whether you wish to support a religion through your shopping, in the case of Halal Certification then the religion you support is Islam.

Sure many people don't care, however many do - both are equally within their rights to do so.
I can assure you Islamic organisations aren't about to donate their hard earned to Atheist organisations, and likewise most Atheists object to the funding of Islam through food etc. The issue with labelling is that more and more companies that pay for certification, are working to hide this information from the larger community. That practice needs to stop.