The following is for a freelancer and entrepreneur-
The Govt's site is complex for entrepreneurs (self-employed people) or small companies. And so is ClearTax (because of the complex rules). For that ClearTax has a blog that is pretty helpful in understanding the system and places your trust on them. But when I dived into the details ClearTax makes things sound so simple and increases your procedures and you end up paying unnecessary tax. Luckily when I started I had evaluated ClearTax and also liked it - its when I get into the details (the fine print of tax-laws) that my trust eroded off ClearTax.
ClearTax is also costlier than consulting a local practising CA (1.5 - 2x). However finding a good CA (or CA firm) and getting comfortable with them is a challenge. And it is worth pursuing the challenge. Even if I had to start again, I would consult a local CA. Also a good CA can help you save money and/or taxes (in legal ways). Apart from that I have heard that ClearTax has operational problems (like they miss out on filing returns when they are overloaded) - This last part is just from references and ClearTax might have solved it.
Note that the tax-laws for businesses in India are way complex and it is hard to understand those. Add to that the changes that occur every few years and the multiple tax authorities. The country rightly deserves the "difficult to do biz" tag. Many CAs err (or are just unsure) and you end up paying more tax than what was actually required. I would place ClearTax in that category.