The tweeters on the A pillars are probably your problem.
My 2005 Accord has the tweeters in the dash corners pointed at the windshield, a terrible location that causes a horn effect between the windshield and the dash. A 15 minute ride at moderate volume would give me a headache.
My temporary solution was fast food napkins over them, a vast improvement. A thick hat worn over the ears is also effective. I do have a screwdriver gouge in the dash near one where I tried to pry one out in a fit of frustration.
Leaving the stereo on overnight a few times and turning the treble way down until they were broken in seems to have worked.
At present the treble and bass are at -2 and 0, and the sound is quite good for a factory stereo. Not in a detailed or accurate way, but fairly balanced and a slightly plump midbass to add some thump to my dance music. I also noticed that the audio system seems to be equalized differently for different sources, when listening to FM, there is an intolerable bass boost that sounds so unnatural that it is unpleasant. Perhaps you could check different sources and see if yours is similar.
I think you should stick some black felt over the tweeters for a while until they break in.