Mouse players are going to have supreme disadvantage against touchscreen players. Also it's going to depend on your exact mouse and mouse settings. If you're going to do a rhythm game it's better to make it a keyboard game but just beware of key ghosting and make sure your game doesn't ghost on even cheap keyboards.
Rhythm is likely going to be off or not perfect and this has to do both with the rhythm skills of the creator of the stages and also system-specific differences such as what browser a player is using or what audio setup a player has. A simple fix for the system differences is just include some sort of calibration feature, such as games typically provided for joysticks to account for differences in joysticks, for example. It won't fix the creator's rhythm being off at any of the stage parts though. There are ways you could design the stages such that the rhythm would never be off on the creator's part by using audio analysis type software to find exactly where the beats are and then line everything up according to that. Not sure if you did that or not.
I'm not a fan of rhythm games penalizing for combo breaking. Score should be a factor entirely of accuracy and zero amount of combo. For example if your accuracy is flawless but you miss exactly one, you could have a significantly lower score than someone whose accuracy was garbage but yet who hit them all. Clearly the first person is a much better player than the second though! Or your score could vary wildly based on exactly which note you missed! Combos work well in fighting games, not rhythm games.