Not 'should they pay taxes' (of course, those which are owed, not doing so is evasion and illegal) but 'how should they be taxed'.
Tax laws apply to them, but pretty much (IANA tax professional btw) aren't setup for online companies and haven't changed (in rough form) since they existed.
Profit based taxation doesn't work if you can just continually reinvest revenue and not declare a profit. (Not unique to online cos of course, but perhaps more prevalent? Maybe more linked to high R&D cos in general.)
Defining where a sale was conducted is messy if your headquarters, accounting dept., tech dept., servers, TLD, customer, self-identity, ... can all be in different jurisdictions.
Etc. ad nauseam. That's what's up for debate.
I think we'd be happy with the same outcome, I just don't think it's worth appealing to companies to ignore the bottom line and pay tax to a level that's higher than required (and so not defined) but that 'we' (you'll never please everyone, so pluck a number out of the air) will be happy with.