How does the first amendment protect five basic freedoms?

If you break the First Amendment down, it is easier to see what it does as a whole:

1. Congress shall make no law respecting an establishment of religion,
2. or prohibiting the free exercise thereof;
3. or abridging the freedom of speech,
4. or of the press;
5. or the right of the people peaceably to assemble,
6. and to petition the Government for a redress of grievances.

As you can see there are MORE than 5 protections; modernised in its language it is:

1. Congress cannot establish a religion - IE: congress cannot promote any religion over another.
2. Congress cannot limit a religion or its practice - except where that religion would violate the rights of others (human sacrifice, passing laws based on religion (noted by Jefferson to be subversion))
3. Congress cannot make it unlawful to say things or use Words it does not approve of except where that speech is intended to commit a crime against another (or cause it to be committed.
4. The press (books and papers) could not be limited anymore than speech; except that the press has a special duty to be truthful in their reports.
5. The right of the people to form groups for political reasons; a key element in maintaining our control of government is in the formation of these groups.
6. This part is a very involved part (James Madison commissioned John Story to write a book on this part), its intent was to ensure that the people always had a way to keep control of government (it is a very large book).