"Can't help but think" means that despite your best efforts, you find yourself unable to stop a particular thought or feeling. It implies that the thought or feeling arises naturally and involuntarily, according to plainenglish.com. 
 
In simpler terms: It means something is happening (a thought, a feeling, an observation) that you can't prevent from happening. You can't "help" it, meaning you can't stop yourself from having that thought or feeling.