You're right - the tom is very hard to pull out. The only time I can hear it in isolation seems to be right at the end where, to my ears, it sounds thin and boxy. It feels like it's missing thump and attack. Are you able to bring the instrument or sample level up relative to the other elements in the mix?
It has some overlapping frequencies with the kick, but you have them rhythmically separated so that may not be a problem. Are you compressing the tom? I'd think you'd want to go light (slow attack speed, less than -6dB reduction) or not-at-all with compression on tom sounds. You want to keep the attack crisp.
Check your eq on the tom - the boxy sound may be around ~300Hz, so you might want to cut there and boost the overall level for the sound.
