I’ve come across many guitarists in my time who don’t have a great sense of rhythm. I believe this is because they’ve skipped the fundamentals of rhythm and learning to count, and focused more on melody and lead playing instead.
Something that will help your rhythm playing greatly is learning drum rhythms, while just playing one note or chord. Syncopation for the Modern Drummer is an excellent book for practising this. By incorporating this into your practice routine, you’ll be spending some time focusing solely on rhythm – a must for every guitarist.