1. Loving one's country is much different from loving one's government. Remember, this was an era when lots of people were overthrowing their own governments in the name of patriotism.
2. How long would it take the other fleets to return home to fight Nelson? Several months at least and they probably wouldn't be in prime fighting condition when they got there.
3. From what I've read about Nelson, he had the unquestioned loyalty and discipline of his men. And they were of the lowest class of British society. In a rebellion they had little to lose and much to gain. Officers who wouldn't go along could be bribed, threatened or replaced.
4. Building ships and building a battle fleet are two different things. Everyone knew that if the French/Spanish fleet were destroyed, it would be a very long time before a naval force that could defeat the British in a standard battle could be constructed.
5. Nelson had the opportunity (whether he had the will is up for debate) to threaten the status quo of British society. Parliament had two options; pray that he didn't or kill him while they had the chance.
Again, I'm not suggesting that Nelson was planning a coup. I'm saying Parliament saw him as much more dangerous than he was useful. I believe that they decided to take a "Better safe than sorry" approach to the situation.
1) Yes, but not in Britain (with the exception of Ireland). Nelson did not support the mutinies in the Royal Navy in 1797, which were largely down to poor rates of pay. Revolutions at this time are seen as Jacobinism - a no-no in the UK at the time.
2) Well for a start there's the Channel Fleet, commanded by William Cornwallis. He detached forces to send to Nelson and was a very competant naval commander.
3) Yes, his men were loyal to Nelson, but anything that smelled of revolution would be labelled Jacobinism - and there would have been ructions.
4) Large French forces were still being blockaded by the Royal Navy in French ports.
5) I really don't think that Parliament saw him as being dangerous, I really don't. He wasn't a political admiral, he didn't speak out about land reform of the Irish Question, or even Catholic Emancipation IIRC.