Estou com febre, por isso vou ficar em casa hoje.

Because estar is used for temporary states or conditions, and having a fever is temporary.

• estou com febre = I have a fever / I’m running a fever
• sou comes from ser, which is used for more permanent characteristics, identity, profession, origin, and so on.

So sou com febre would be wrong.

In Brazilian Portuguese, estar com is very common for temporary physical conditions:

• estar com febre = to have a fever
• estar com dor de cabeça = to have a headache
• estar com sono = to be sleepy
• estar com fome = to be hungry

You may sometimes hear tenho febre, but estou com febre sounds more natural when talking about your current condition right now.

Normally com means with, but in this kind of expression it helps describe a condition someone is experiencing.

So estou com febre literally looks like I am with fever, but the natural English meaning is I have a fever.

This is a very common pattern in Portuguese, so it is worth getting used to it.

Por isso means therefore, because of that, or that’s why.

In this sentence, it connects the two ideas:

• Estou com febre = I have a fever
• por isso vou ficar em casa hoje = that’s why I’m going to stay home today

It is a natural way to show cause and result.

Other similar connectors are:

• então = so
• por causa disso = because of that
• por esse motivo = for that reason

Vou ficar is the very common spoken way to express the future in Brazilian Portuguese.

It uses:

• ir in the present tense
• • infinitive verb

So:

• vou ficar = I’m going to stay / I will stay

You could also say ficarei, which is the simple future, but in everyday Brazilian speech vou ficar sounds more natural and conversational.

Ficar often means to stay, to remain, or to end up depending on the context.

Here, ficar em casa means to stay at home.

Examples:

• Vou ficar em casa. = I’m going to stay home.
• Ela ficou no trabalho até tarde. = She stayed at work until late.
• Ficamos cansados. = We became tired.

So in this sentence, ficar has the idea of remaining somewhere.

Em casa is the normal expression for at home.

• em casa = at home
• na casa de alguém = at someone’s house

So:

• Vou ficar em casa hoje. = I’m going to stay home today.
• Vou ficar na casa da minha irmã. = I’m going to stay at my sister’s house.

English speakers often want to translate home too literally, but em casa is the fixed everyday expression.

Yes, hoje can move around. Portuguese is fairly flexible with adverbs like this.

These are all possible:

• Hoje vou ficar em casa.
• Vou ficar em casa hoje.
• Vou hoje ficar em casa. ← possible, but less natural here

The version in your sentence sounds very natural. Putting hoje at the end often feels smooth and conversational.

In careful speech, it is:

Estou com febre, por isso vou ficar em casa hoje.

In natural Brazilian speech, a few things often happen:

• estou may sound closer to tô in casual speech
• para often reduces to pra, though that word is not in this sentence
• rhythm is smooth, and unstressed vowels may sound lighter

A very natural casual version would be:

Tô com febre, por isso vou ficar em casa hoje.

That said, estou is completely correct and a bit more neutral or careful.

Yes, often you can.

• Estou com febre, por isso vou ficar em casa hoje.
• Estou com febre, então vou ficar em casa hoje.

Both are natural.

The difference is small:

• por isso feels a little more explicitly like for that reason
• então feels more like so

In everyday conversation, então is very common.

Yes. A very natural casual version would be:

Tô com febre, então vou ficar em casa hoje.

Changes:

• estou → tô
• por isso → então

The meaning stays the same, but it sounds more informal and conversational. The original sentence is still perfectly natural and correct.