Not sure what BC level your at but I'll try and help, although what you've been doing seems fairly close.
When I'm listening to something, opposed to trying to learn a new piece, I can easily hear what is 4 beats per bar (1234) and what is either 3 or 6 beats per bar. For example try counting 12341234etc to a waltz and you'll see that it quickly goes out of sync. So my original question was really how do I identify the 1234 beat of the song (a little more knowledge help me phrase that better than the original post
Shadow and Mike's answer go a long way to help, when you are just listening to a track.
For most pop, rock, blues stuff the bass drum pulse is on 1 and 3, with the snare drum pulse on 2 and 4.
Thump, tok, thump, tok = 1 2 3 4
That is gonna get you there 80% of the time. As always there are variations, but that is a great place to start. Shadow
Like shadow said, the kick and the snare tend to drive the tempo of the song. I find that if I tap your foot or nod my head along to a song, it usually matches up to the beat and I can work out the tempo from there.
I listen to a lot of high energy, fast rhythm rock and when I'm foot tapping its always at a hundred miles an hour, especially if I'm really into it. But I'm learning to play songs, I'm beginning to listen and analyse differently. I would find myself tapping away thinking these must be fastly played bars say of 12341234123412341234 ie 4 quick bars of 4 strums when whats actually being played was 1+2+3+4+1+2+3+4+ 2 bars of 8 strums.
If you've learnt or are learning stage 1 songs its a bit like the difference between Three Little Birds and Common People. With TLB your strumming 4 beats to the bar 1234 //// AAAA AAAA DDDD AAAA so you're foot tapping would sync with the strums or vice versa.
Common People played along with the records is 'pumping 8s' as Justin calls it ie 8 beats to the bar.
So when your tapping 1234 you are actually playing two down strums per tap, the 2nd being when the foot is raised and about to come down. This where the 1+2+3+4+ comes in ie 8 beats. If you think tap/raise/tap/raise/tap/raise/tap/raise you strum not only when you tap but when the foot is up.
When you come to learn the strumming patterns in RUST you'll see this falls into place with the introduction of the Up strum, which JS covers when he covers the strumming patterns of the part one songs. You could have a bar of DUDUDUDU (1+2+3+4+), when you listen to music you'll hear the up strums standing out, as they're not a full as the down strum, as you only hit 3 or 4 strings on the up.
What I've just started doing and this may help you (and others) is to start moving my strumming hand along with my foot when listening to something. Doing this I get a feel for the up strums and it also helps to identify the strumming pattern being played. I get a better idea of where the 1 2 3 4 falls and from there its easy to get a better idea of the BPM.
An example of how to get it wrong was my recent post of Whats Up. Read that threads and see the difference it made trying to play the song at 135bpm rather than 63bpm. http://justinguitarcommunity.com/index.php?topic=35538.15
half way down page 2
You'll sense that somethings not quite right. Finally watching a video of the song often helps, the bands foot tapping, body movement and strumming.
Hope you find this helpful