Sedition, the technical legal term for what you're talking about, is prohibited by section 124A of the Indian Penal Code (IPC). This dates all the way back to the colonial era, and was originally used to suppress people pushing for India's independence from Britain.

The Supreme Court of India ruled in 1962 that section 124A was constitutional, but that speech or actions only constitute sedition if it incites or tends to incite violence or disorder. There is apparently some ongoing issues with this, with allegations of various substance that people are being charged with sedition despite their speech and/or actions not meeting this standard. But that's not terribly relevant to your question, though it might explain why it is of importance to you.

Answering your question beyond that is difficult, however. Free speech is enshrined in India's constitution, and indeed in several international treaties and conventions that India is a part of. But the jurisprudence on the matter seems inconsistent, with courts of all levels (including the Supreme Court) tending to produce conflicting precedents. The simplest explanation may be historical momentum: this part of the IPC has been around for a long time, and it can be difficult to repeal or alter (or, at times, even find) laws that are so old. This gets exacerbated by the idea that, in principle, Supreme Court decisions have already made alterations to the law, and legislatures across the globe tend to be slow to make such formal alterations. This is apparent in the United States, too, where many laws, state constitutions, etc. formally contain provisions that have been held unconstitutional. These have no legal force, and nobody tries to enforce them, so formally altering them is basically just political theater to most people (though technically, if the US constitution was suitably amended they could be rendered valid once again), and so time better spent elsewhere.

I'm not familiar with India, but in general, guaranteed freedoms are never absolute. This would be a recipe for anarchy. The enforcing authority (the government) has to limit every freedom at least a little, or else that freedom could then be used to infringe upon other freedoms.

In the US, freedom of speech is pretty sacred and generally interpreted by the courts very expansively -- that's why it's so hard in the US to sue someone for libel or prosecute someone for treason. But even in the US there are serious limitations. As a basic example, it is illegal to use speech to directly incite a crime.

Governments Crave Self-Preservation

The degree may vary, but all sufficiently large organisations eventually start gaining traits that promote its preservation. Some see it as a government's duty to ensure it doesn't get toppled easily, others will point out that governments without such measures are likely to, in the long run, be toppled more often, leading to an evolutionary selection of sorts for governments with such measures.

Restrictions on speech against inciting a toppling of a government are one example of such measure. (Others include monopoly on military force, on legislation and enforcement of law etc.)

In a democracy, you are allowed to advocate a complete overthrow of the existing government, via voting. While it is commonplace today, the peaceful transfer of power from one government to the next is just that - an existing government stepping down and allowing itself to be overthrown.

What you can't do is advocate violence, whether to overthrow a government or any other reason, because advocating a crime is generally not considered protected speech.

Since I have found that most of the answers are not India specific, I am adding to them.
In India we derive freedom of speech and expression from Article 19 (1) (a). This freedom is (like all the other 5) subjected to reasonable restrictions, 19 (2) specifically on freedom of speech. Clause (2) of the article puts 8 restriction on freedom of speech namely,

1. Sovereignty and integrity of state


2. Security of state


3. Friendly relations with foreign states


4. Public order


5. Decency or morality


6. Contempt of court


7. Defamation


8. Incitement of offence

If your speech is not hurting any of these then you're good and can oppose the government but inciting to rebel threatens point 1 IF government is legally established (as it has people's mandate) and also point 8 to some extent (IPC Section 124A, but it's removal is debated).
As sovereignty and democracy are basic elements of our constitution (Kesavanand Bharati case) it can't be amended and hence as long as democracy and rule of law is there you can't incite to rebel against a just and democratically elected government.

Because there is a law prohibiting it!

'Free Speech' is an ideal. Many constitutions, written or unwritten, set great store by it.

But no country I know of allows unlimited free speech. They all draw the line when it is misrepresentation, harmful, obscene, incitement to criminal action etc.

I know we're discussing India. But it is interesting to consider whether America's beloved Second Amendment, often interpreted as enabling citizens to overthrow a tyrannical government, implies freedom to discuss and advocate such an action.