Why? There are those that like the knight Sir Glenn, you know. And mighty Crono is not much less liked than that fabled sorcerer. After all, while the wizard might win in a battle of wits, in battle-cunning, deftness of hand and in the skill of weaponry, though Janus is quite the master, Crono outmatches him - even the sigaldry of Janus cannot contend against the holy magic of the prince of time. And even if the dark one's strength was greater than Crono's... he lacks the patience to strike when the timing is best, and his wrath and pride turn his power against him. Think even in weaponry - why does Janus use a scythe? Fear and power, but it is not a good weapon, not nearly so good as a falchion-blade. Though, mythically speaking, I think it would be more apt if it were Crono that bore the sickle, as his namesake did, but that is a different matter...
Yes, I am speaking in battle-skill, I know that well enough. But even as far as character goes, Crono is not at a full disadvantage. If those that like Janus only for his superficial, seemingly 'cool', darkness, could be swayed, the scales would tip decidedly in Crono's favour.