If you focus too much on ending syllables on the snare, you wil come off sounding robotic, unnatural and uncomfortable. However, if you're having trouble catching the beat in the first place, that's probably still a good starting place. Just be aware that once you get there, you will need to work towards sounding natural on the beat.

If every MC rhymed along with the kick and snare in the way you're talking about, rap would get boring very fast. You are correct in seeing the relationship between kick, snare, and the timing of words, but ending on the snare is just one of many possible relationships. The idea is that there needs to be SOME kind of relationship for things to sound correct.

Music is all about patterns. When you combine two patterns with compatible timing, a larger pattern will be formed. Your voice should form a larger pattern with the music. When you rhyme along with the guitar (or whatever else) you may be making a pattern with that instrument, which is fine, but it's not sounding good because there is no pattern between you and the drums. The WHOLE pattern needs to work. We tend to use the drum to guide us because as Aeon said, it usually controls the rhythm and timing of the song. If every element is in a pattern with the drums, they will be in a pattern with each other too. Rhyming with the non rhythm instruments can really improve your flow. It is not something you should try to avoid. You just have to make sure that when you do it you are still in a pattern with the drums.

So when I'm hearing your verse, I should be able to tell that there is a deliberate pattern between the lyrics and the music. Try messing around with some different patterns to get a sense of what I'm talking about. Try ending every line on the first kick of the beat. Try stressing the syllables on the off beats (the beat between the kick and the snare). experiment with other patterns. Once you start getting comfortable with that, you can try throwing multiple patterns into one verse. Many MCs shift from pattern to pattern in one verse. That is why with some of them you have a hard time hearing exactly how they are matching up with the kick/snare.