I think you're trying to run before you can walk.
In Bass Guitar for Dummies, Patrick Pfeiffer discusses exactly this topic and guides the reader to note choices that work both on important rhythm nodes (I mean points in the bar where the rhythm lies, not necessarily beat 1 or 3 specifically) and less important ones (where no one else is playing). So, for example don't start your bar with the second note of the chord but you can slide down to it later on in the bar and then on to the root, or alternatively don't over-emphasise the sixth but you could mute it and move quickly to the fifth.
Try starting on the appropriate third and walking up to the next chord via important chord tones on the drum beats (eg E, C, d-> G, F). If you're moving from C down to Em, you could finish your C bar on the F above E and then be on E for the start of the E bar. I recommend to you Ed Friedland's "Walking Bass". He does this in spades and in all keys so you really, really get it.
Most importantly, listen to the drums and choose when to match the beats with notes and when to leave them space and play in the spaces left by them. The only way to learn this is to play with a thoughtful drummer, or to listen to a lot of music with your headphones on. The phrase that needs to run through your head as you listen is "that part really worked, so why exactly...." and listen again. You won't gain this kind of tastefulness from watching Youtube.